Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome
The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the di...
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ftunivutrecht:oai:dspace.library.uu.nl:1874/409800 2023-12-03T10:30:19+01:00 Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome Coutinho, F H von Meijenfeldt, F A B Walter, J M Haro-Moreno, J M Lopéz-Pérez, M van Verk, M C Thompson, C C Cosenza, C A N Appolinario, L Paranhos, R Cabral, A Dutilh, B E Thompson, F L Theoretical Biology and Bioinformatics Sub Bioinformatics 2021-04-15 application/pdf https://dspace.library.uu.nl/handle/1874/409800 en eng 0048-9697 https://dspace.library.uu.nl/handle/1874/409800 info:eu-repo/semantics/OpenAccess South Atlantic Ocean Bathypelagic Metagenomics Metagenome assembled genomes Viruses Taverne Article 2021 ftunivutrecht 2023-11-08T23:19:57Z The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean. Article in Journal/Newspaper South Atlantic Ocean Utrecht University Repository Calvin ENVELOPE(165.100,165.100,-71.283,-71.283) |
institution |
Open Polar |
collection |
Utrecht University Repository |
op_collection_id |
ftunivutrecht |
language |
English |
topic |
South Atlantic Ocean Bathypelagic Metagenomics Metagenome assembled genomes Viruses Taverne |
spellingShingle |
South Atlantic Ocean Bathypelagic Metagenomics Metagenome assembled genomes Viruses Taverne Coutinho, F H von Meijenfeldt, F A B Walter, J M Haro-Moreno, J M Lopéz-Pérez, M van Verk, M C Thompson, C C Cosenza, C A N Appolinario, L Paranhos, R Cabral, A Dutilh, B E Thompson, F L Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome |
topic_facet |
South Atlantic Ocean Bathypelagic Metagenomics Metagenome assembled genomes Viruses Taverne |
description |
The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean. |
author2 |
Theoretical Biology and Bioinformatics Sub Bioinformatics |
format |
Article in Journal/Newspaper |
author |
Coutinho, F H von Meijenfeldt, F A B Walter, J M Haro-Moreno, J M Lopéz-Pérez, M van Verk, M C Thompson, C C Cosenza, C A N Appolinario, L Paranhos, R Cabral, A Dutilh, B E Thompson, F L |
author_facet |
Coutinho, F H von Meijenfeldt, F A B Walter, J M Haro-Moreno, J M Lopéz-Pérez, M van Verk, M C Thompson, C C Cosenza, C A N Appolinario, L Paranhos, R Cabral, A Dutilh, B E Thompson, F L |
author_sort |
Coutinho, F H |
title |
Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome |
title_short |
Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome |
title_full |
Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome |
title_fullStr |
Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome |
title_full_unstemmed |
Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome |
title_sort |
ecogenomics and metabolic potential of the south atlantic ocean microbiome |
publishDate |
2021 |
url |
https://dspace.library.uu.nl/handle/1874/409800 |
long_lat |
ENVELOPE(165.100,165.100,-71.283,-71.283) |
geographic |
Calvin |
geographic_facet |
Calvin |
genre |
South Atlantic Ocean |
genre_facet |
South Atlantic Ocean |
op_relation |
0048-9697 https://dspace.library.uu.nl/handle/1874/409800 |
op_rights |
info:eu-repo/semantics/OpenAccess |
_version_ |
1784256080332718080 |