Eukaryotic richness in the abyss: insights from pyrotag sequencing
Background: The deep sea floor is considered one of the most diverse ecosystems on Earth. Recent environmental DNA surveys based on clone libraries of rRNA genes confirm this observation and reveal a high diversity of eukaryotes present in deep-sea sediment samples. However, environmental clone-libr...
Published in: | PLoS ONE |
---|---|
Main Authors: | , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Public Library of Science
2011
|
Subjects: | |
Online Access: | http://hdl.handle.net/10400.1/11131 https://doi.org/10.1371/journal.pone.0018169 |
id |
ftunivalgarve:oai:sapientia.ualg.pt:10400.1/11131 |
---|---|
record_format |
openpolar |
spelling |
ftunivalgarve:oai:sapientia.ualg.pt:10400.1/11131 2023-05-15T15:02:18+02:00 Eukaryotic richness in the abyss: insights from pyrotag sequencing Pawlowski, Jan Christen, Richard Lecroq, Beatrice Bachar, Dipankar Shahbazkia, Hamid R. Amaral-Zettler, Linda Guillou, Laure 2011-04 http://hdl.handle.net/10400.1/11131 https://doi.org/10.1371/journal.pone.0018169 eng eng Public Library of Science SNSF /Project funding 1932-6203 http://hdl.handle.net/10400.1/11131 doi:10.1371/journal.pone.0018169 openAccess http://creativecommons.org/licenses/by/4.0/ CC-BY Eastern mediterranean sea Deep-sea Microbial Eukaryotes Cercozoa Protozoa Rare biosphere Arctic-ocean Cold-seep Diversity Dna Biodiversity article 2011 ftunivalgarve https://doi.org/10.1371/journal.pone.0018169 2022-05-30T08:48:11Z Background: The deep sea floor is considered one of the most diverse ecosystems on Earth. Recent environmental DNA surveys based on clone libraries of rRNA genes confirm this observation and reveal a high diversity of eukaryotes present in deep-sea sediment samples. However, environmental clone-library surveys yield only a modest number of sequences with which to evaluate the diversity of abyssal eukaryotes. Methodology/Principal Findings: Here, we examined the richness of eukaryotic DNA in deep Arctic and Southern Ocean samples using massively parallel sequencing of the 18S ribosomal RNA (rRNA) V9 hypervariable region. In very small volumes of sediments, ranging from 0.35 to 0.7 g, we recovered up to 7,499 unique sequences per sample. By clustering sequences having up to 3 differences, we observed from 942 to 1756 Operational Taxonomic Units (OTUs) per sample. Taxonomic analyses of these OTUs showed that DNA of all major groups of eukaryotes is represented at the deep-sea floor. The dinoflagellates, cercozoans, ciliates, and euglenozoans predominate, contributing to 17%, 16%, 10%, and 8% of all assigned OTUs, respectively. Interestingly, many sequences represent photosynthetic taxa or are similar to those reported from the environmental surveys of surface waters. Moreover, each sample contained from 31 to 71 different metazoan OTUs despite the small sample volume collected. This indicates that a significant faction of the eukaryotic DNA sequences likely do not belong to living organisms, but represent either free, extracellular DNA or remains and resting stages of planktonic species. Conclusions/Significance: In view of our study, the deep-sea floor appears as a global DNA repository, which preserves genetic information about organisms living in the sediment, as well as in the water column above it. This information can be used for future monitoring of past and present environmental changes. French ANR Aquaparadox; ANR DeepOases; Swiss National Science Foundation [31003A-125372]; WM Keck foundation ... Article in Journal/Newspaper Arctic Arctic Ocean Southern Ocean Universidade do Algarve: Sapienta Arctic Arctic Ocean Southern Ocean PLoS ONE 6 4 e18169 |
institution |
Open Polar |
collection |
Universidade do Algarve: Sapienta |
op_collection_id |
ftunivalgarve |
language |
English |
topic |
Eastern mediterranean sea Deep-sea Microbial Eukaryotes Cercozoa Protozoa Rare biosphere Arctic-ocean Cold-seep Diversity Dna Biodiversity |
spellingShingle |
Eastern mediterranean sea Deep-sea Microbial Eukaryotes Cercozoa Protozoa Rare biosphere Arctic-ocean Cold-seep Diversity Dna Biodiversity Pawlowski, Jan Christen, Richard Lecroq, Beatrice Bachar, Dipankar Shahbazkia, Hamid R. Amaral-Zettler, Linda Guillou, Laure Eukaryotic richness in the abyss: insights from pyrotag sequencing |
topic_facet |
Eastern mediterranean sea Deep-sea Microbial Eukaryotes Cercozoa Protozoa Rare biosphere Arctic-ocean Cold-seep Diversity Dna Biodiversity |
description |
Background: The deep sea floor is considered one of the most diverse ecosystems on Earth. Recent environmental DNA surveys based on clone libraries of rRNA genes confirm this observation and reveal a high diversity of eukaryotes present in deep-sea sediment samples. However, environmental clone-library surveys yield only a modest number of sequences with which to evaluate the diversity of abyssal eukaryotes. Methodology/Principal Findings: Here, we examined the richness of eukaryotic DNA in deep Arctic and Southern Ocean samples using massively parallel sequencing of the 18S ribosomal RNA (rRNA) V9 hypervariable region. In very small volumes of sediments, ranging from 0.35 to 0.7 g, we recovered up to 7,499 unique sequences per sample. By clustering sequences having up to 3 differences, we observed from 942 to 1756 Operational Taxonomic Units (OTUs) per sample. Taxonomic analyses of these OTUs showed that DNA of all major groups of eukaryotes is represented at the deep-sea floor. The dinoflagellates, cercozoans, ciliates, and euglenozoans predominate, contributing to 17%, 16%, 10%, and 8% of all assigned OTUs, respectively. Interestingly, many sequences represent photosynthetic taxa or are similar to those reported from the environmental surveys of surface waters. Moreover, each sample contained from 31 to 71 different metazoan OTUs despite the small sample volume collected. This indicates that a significant faction of the eukaryotic DNA sequences likely do not belong to living organisms, but represent either free, extracellular DNA or remains and resting stages of planktonic species. Conclusions/Significance: In view of our study, the deep-sea floor appears as a global DNA repository, which preserves genetic information about organisms living in the sediment, as well as in the water column above it. This information can be used for future monitoring of past and present environmental changes. French ANR Aquaparadox; ANR DeepOases; Swiss National Science Foundation [31003A-125372]; WM Keck foundation ... |
format |
Article in Journal/Newspaper |
author |
Pawlowski, Jan Christen, Richard Lecroq, Beatrice Bachar, Dipankar Shahbazkia, Hamid R. Amaral-Zettler, Linda Guillou, Laure |
author_facet |
Pawlowski, Jan Christen, Richard Lecroq, Beatrice Bachar, Dipankar Shahbazkia, Hamid R. Amaral-Zettler, Linda Guillou, Laure |
author_sort |
Pawlowski, Jan |
title |
Eukaryotic richness in the abyss: insights from pyrotag sequencing |
title_short |
Eukaryotic richness in the abyss: insights from pyrotag sequencing |
title_full |
Eukaryotic richness in the abyss: insights from pyrotag sequencing |
title_fullStr |
Eukaryotic richness in the abyss: insights from pyrotag sequencing |
title_full_unstemmed |
Eukaryotic richness in the abyss: insights from pyrotag sequencing |
title_sort |
eukaryotic richness in the abyss: insights from pyrotag sequencing |
publisher |
Public Library of Science |
publishDate |
2011 |
url |
http://hdl.handle.net/10400.1/11131 https://doi.org/10.1371/journal.pone.0018169 |
geographic |
Arctic Arctic Ocean Southern Ocean |
geographic_facet |
Arctic Arctic Ocean Southern Ocean |
genre |
Arctic Arctic Ocean Southern Ocean |
genre_facet |
Arctic Arctic Ocean Southern Ocean |
op_relation |
SNSF /Project funding 1932-6203 http://hdl.handle.net/10400.1/11131 doi:10.1371/journal.pone.0018169 |
op_rights |
openAccess http://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0018169 |
container_title |
PLoS ONE |
container_volume |
6 |
container_issue |
4 |
container_start_page |
e18169 |
_version_ |
1766334272061308928 |