Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current
Microbes occupy diverse ecological niches and only through recent advances in next generation sequencing technologies have the true microbial diversity been revealed. Furthermore, lack of perceivable marine barriers to genetic dispersal (i.e., mountains or islands) has allowed the speculation that o...
Published in: | Frontiers in Microbiology |
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Uppsala universitet, Limnologi
2018
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Online Access: | http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-361693 https://doi.org/10.3389/fmicb.2018.01474 |
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ftuppsalauniv:oai:DiVA.org:uu-361693 2024-02-11T09:58:38+01:00 Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current Flaviani, Flavia Schroeder, Declan C. Lebret, Karen Balestreri, Cecilia Highfield, Andrea C. Schroeder, Joanna L. Thorpe, Sally E. Moore, Karen Pasckiewicz, Konrad Pfaff, Maya C. Rybicki, Edward P. 2018 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-361693 https://doi.org/10.3389/fmicb.2018.01474 eng eng Uppsala universitet, Limnologi Univ Cape Town, Biopharming Res Unit, Dept Mol & Cell Biol, Cape Town, South Africa;Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England Univ Reading, Sch Biol Sci, Reading, Berks, England;Univ Minnesota Twin Cities, Coll Vet Med, Minneapolis, MN 55455 USA;Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England Marine Biol Assoc UK, Citadel Hill, Plymouth, Devon, England NERC, British Antarctic Survey, Cambridge, England Univ Exeter, Exeter Sequencing Serv, Biosci, Exeter, Devon, England Oceans & Coasts, Dept Environm Affairs, Cape Town, South Africa Univ Cape Town, Biopharming Res Unit, Dept Mol & Cell Biol, Cape Town, South Africa FRONTIERS MEDIA SA Frontiers in Microbiology, 2018, 9, orcid:0000-0002-3853-1662 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-361693 doi:10.3389/fmicb.2018.01474 ISI:000438921400001 info:eu-repo/semantics/openAccess Antarctic Polar Front marine microbes eDNA meDNA viruses microbiome Microbiology Mikrobiologi Article in journal info:eu-repo/semantics/article text 2018 ftuppsalauniv https://doi.org/10.3389/fmicb.2018.01474 2024-01-17T23:33:44Z Microbes occupy diverse ecological niches and only through recent advances in next generation sequencing technologies have the true microbial diversity been revealed. Furthermore, lack of perceivable marine barriers to genetic dispersal (i.e., mountains or islands) has allowed the speculation that organisms that can be easily transported by currents and therefore proliferate everywhere. That said, ocean currents are now commonly being recognized as barriers for microbial dispersal. Here we analyzed samples collected from a total of six stations, four located in the Indian Ocean, and two in the Southern Ocean. Amplicon sequencing was used to characterize both prokaryotic and eukaryotic plankton communities, while shotgun sequencing was used for the combined environmental DNA (eDNA), microbial eDNA (meDNA), and viral fractions. We found that Cyanobacteria dominated the prokaryotic component in the South-West Indian Ocean, while gamma-Proteobacteria dominated the South-East Indian Ocean. A combination of gamma- and alpha-Proteobacteria dominated the Southern Ocean. Alveolates dominated almost exclusively the eukaryotic component, with variation in the ratio of Protoalveolata and Dinoflagellata depending on station. However, an increase in haptophyte relative abundance was observed in the Southern Ocean. Similarly, the viral fraction was dominated by members of the order Caudovirales across all stations; however, a higher presence of nucleocytoplasmic large DNA viruses (mainly chloroviruses and mimiviruses) was observed in the Southern Ocean. To our knowledge, this is the first that a statistical difference in the microbiome (from viruses to protists) between the subtropical Indian and Southern Oceans. We also show that not all phylotypes can be found everywhere, and that meDNA is not a suitable resource for monitoring aquatic microbial diversity. Article in Journal/Newspaper Antarc* Antarctic Southern Ocean Uppsala University: Publications (DiVA) Antarctic Southern Ocean The Antarctic Indian Frontiers in Microbiology 9 |
institution |
Open Polar |
collection |
Uppsala University: Publications (DiVA) |
op_collection_id |
ftuppsalauniv |
language |
English |
topic |
Antarctic Polar Front marine microbes eDNA meDNA viruses microbiome Microbiology Mikrobiologi |
spellingShingle |
Antarctic Polar Front marine microbes eDNA meDNA viruses microbiome Microbiology Mikrobiologi Flaviani, Flavia Schroeder, Declan C. Lebret, Karen Balestreri, Cecilia Highfield, Andrea C. Schroeder, Joanna L. Thorpe, Sally E. Moore, Karen Pasckiewicz, Konrad Pfaff, Maya C. Rybicki, Edward P. Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current |
topic_facet |
Antarctic Polar Front marine microbes eDNA meDNA viruses microbiome Microbiology Mikrobiologi |
description |
Microbes occupy diverse ecological niches and only through recent advances in next generation sequencing technologies have the true microbial diversity been revealed. Furthermore, lack of perceivable marine barriers to genetic dispersal (i.e., mountains or islands) has allowed the speculation that organisms that can be easily transported by currents and therefore proliferate everywhere. That said, ocean currents are now commonly being recognized as barriers for microbial dispersal. Here we analyzed samples collected from a total of six stations, four located in the Indian Ocean, and two in the Southern Ocean. Amplicon sequencing was used to characterize both prokaryotic and eukaryotic plankton communities, while shotgun sequencing was used for the combined environmental DNA (eDNA), microbial eDNA (meDNA), and viral fractions. We found that Cyanobacteria dominated the prokaryotic component in the South-West Indian Ocean, while gamma-Proteobacteria dominated the South-East Indian Ocean. A combination of gamma- and alpha-Proteobacteria dominated the Southern Ocean. Alveolates dominated almost exclusively the eukaryotic component, with variation in the ratio of Protoalveolata and Dinoflagellata depending on station. However, an increase in haptophyte relative abundance was observed in the Southern Ocean. Similarly, the viral fraction was dominated by members of the order Caudovirales across all stations; however, a higher presence of nucleocytoplasmic large DNA viruses (mainly chloroviruses and mimiviruses) was observed in the Southern Ocean. To our knowledge, this is the first that a statistical difference in the microbiome (from viruses to protists) between the subtropical Indian and Southern Oceans. We also show that not all phylotypes can be found everywhere, and that meDNA is not a suitable resource for monitoring aquatic microbial diversity. |
format |
Article in Journal/Newspaper |
author |
Flaviani, Flavia Schroeder, Declan C. Lebret, Karen Balestreri, Cecilia Highfield, Andrea C. Schroeder, Joanna L. Thorpe, Sally E. Moore, Karen Pasckiewicz, Konrad Pfaff, Maya C. Rybicki, Edward P. |
author_facet |
Flaviani, Flavia Schroeder, Declan C. Lebret, Karen Balestreri, Cecilia Highfield, Andrea C. Schroeder, Joanna L. Thorpe, Sally E. Moore, Karen Pasckiewicz, Konrad Pfaff, Maya C. Rybicki, Edward P. |
author_sort |
Flaviani, Flavia |
title |
Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current |
title_short |
Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current |
title_full |
Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current |
title_fullStr |
Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current |
title_full_unstemmed |
Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current |
title_sort |
distinct oceanic microbiomes from viruses to protists located near the antarctic circumpolar current |
publisher |
Uppsala universitet, Limnologi |
publishDate |
2018 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-361693 https://doi.org/10.3389/fmicb.2018.01474 |
geographic |
Antarctic Southern Ocean The Antarctic Indian |
geographic_facet |
Antarctic Southern Ocean The Antarctic Indian |
genre |
Antarc* Antarctic Southern Ocean |
genre_facet |
Antarc* Antarctic Southern Ocean |
op_relation |
Frontiers in Microbiology, 2018, 9, orcid:0000-0002-3853-1662 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-361693 doi:10.3389/fmicb.2018.01474 ISI:000438921400001 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.3389/fmicb.2018.01474 |
container_title |
Frontiers in Microbiology |
container_volume |
9 |
_version_ |
1790594349146308608 |