Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans
Abstract Background Phytoplankton 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-assemb...
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ftdoajarticles:oai:doaj.org/article:0069a965e3764c518b6126ee9e29cc5b 2023-05-15T14:36:57+02:00 Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans Anthony Duncan Kerrie Barry Chris Daum Emiley Eloe-Fadrosh Simon Roux Katrin Schmidt Susannah G. Tringe Klaus U. Valentin Neha Varghese Asaf Salamov Igor V. Grigoriev Richard M. Leggett Vincent Moulton Thomas Mock 2022-04-01T00:00:00Z https://doi.org/10.1186/s40168-022-01254-7 https://doaj.org/article/0069a965e3764c518b6126ee9e29cc5b EN eng BMC https://doi.org/10.1186/s40168-022-01254-7 https://doaj.org/toc/2049-2618 doi:10.1186/s40168-022-01254-7 2049-2618 https://doaj.org/article/0069a965e3764c518b6126ee9e29cc5b Microbiome, Vol 10, Iss 1, Pp 1-21 (2022) Microbial ecology QR100-130 article 2022 ftdoajarticles https://doi.org/10.1186/s40168-022-01254-7 2022-12-31T03:20:53Z Abstract Background Phytoplankton 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. Results Here, 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. Conclusion Our 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 Directory of Open Access Journals: DOAJ Articles Arctic Microbiome 10 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Microbial ecology QR100-130 |
spellingShingle |
Microbial ecology QR100-130 Anthony Duncan Kerrie Barry Chris Daum Emiley Eloe-Fadrosh Simon Roux Katrin Schmidt Susannah G. Tringe Klaus U. Valentin Neha Varghese Asaf Salamov Igor V. Grigoriev Richard M. Leggett Vincent Moulton Thomas Mock Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans |
topic_facet |
Microbial ecology QR100-130 |
description |
Abstract Background Phytoplankton 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. Results Here, 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. Conclusion Our 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 |
Anthony Duncan Kerrie Barry Chris Daum Emiley Eloe-Fadrosh Simon Roux Katrin Schmidt Susannah G. Tringe Klaus U. Valentin Neha Varghese Asaf Salamov Igor V. Grigoriev Richard M. Leggett Vincent Moulton Thomas Mock |
author_facet |
Anthony Duncan Kerrie Barry Chris Daum Emiley Eloe-Fadrosh Simon Roux Katrin Schmidt Susannah G. Tringe Klaus U. Valentin Neha Varghese Asaf Salamov Igor V. Grigoriev Richard M. Leggett Vincent Moulton Thomas Mock |
author_sort |
Anthony Duncan |
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 |
BMC |
publishDate |
2022 |
url |
https://doi.org/10.1186/s40168-022-01254-7 https://doaj.org/article/0069a965e3764c518b6126ee9e29cc5b |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Phytoplankton |
genre_facet |
Arctic Phytoplankton |
op_source |
Microbiome, Vol 10, Iss 1, Pp 1-21 (2022) |
op_relation |
https://doi.org/10.1186/s40168-022-01254-7 https://doaj.org/toc/2049-2618 doi:10.1186/s40168-022-01254-7 2049-2618 https://doaj.org/article/0069a965e3764c518b6126ee9e29cc5b |
op_doi |
https://doi.org/10.1186/s40168-022-01254-7 |
container_title |
Microbiome |
container_volume |
10 |
container_issue |
1 |
_version_ |
1766309467752759296 |