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Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments

BACKGROUND: Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater e...

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Autores principales: Chambouvet, Aurélie, Berney, Cédric, Romac, Sarah, Audic, Stéphane, Maguire, Finlay, De Vargas, Colomban, Richards, Thomas A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044210/
https://www.ncbi.nlm.nih.gov/pubmed/24779375
http://dx.doi.org/10.1186/1471-2180-14-110
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author Chambouvet, Aurélie
Berney, Cédric
Romac, Sarah
Audic, Stéphane
Maguire, Finlay
De Vargas, Colomban
Richards, Thomas A
author_facet Chambouvet, Aurélie
Berney, Cédric
Romac, Sarah
Audic, Stéphane
Maguire, Finlay
De Vargas, Colomban
Richards, Thomas A
author_sort Chambouvet, Aurélie
collection PubMed
description BACKGROUND: Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples and only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled group in marine environments. Using 454 diversity ‘tag’ sequencing we investigate the diversity and distribution of these protists in marine sediments and water column samples taken from the Deep Chlorophyll Maximum (DCM) and sub-surface using both DNA and RNA as the source template and sampling four European offshore locations. RESULTS: We detected the presence of 265 sequences branching with known Perkinsea, the majority of them recovered from marine sediments. Moreover, 27% of these sequences were sampled from RNA derived cDNA libraries. Phylogenetic analyses classify a large proportion of these sequences into 38 cluster groups (including 30 novel marine cluster groups), which share less than 97% sequence similarity suggesting this diversity encompasses a range of biologically and ecologically distinct organisms. CONCLUSIONS: These results demonstrate that the Perkinsea lineage is considerably more diverse than previously detected in marine environments. This wide diversity of Perkinsea-like protists is largely retrieved in marine sediment with a significant proportion detected in RNA derived libraries suggesting this diversity represents ribosomally ‘active’ and intact cells. Given the phylogenetic range of hosts infected by known Perkinsea parasites, these data suggest that Perkinsea either play a significant but hitherto unrecognized role as parasites in marine sediments and/or members of this group are present in the marine sediment possibly as part of the ‘seed bank’ microbial community.
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spelling pubmed-40442102014-06-05 Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments Chambouvet, Aurélie Berney, Cédric Romac, Sarah Audic, Stéphane Maguire, Finlay De Vargas, Colomban Richards, Thomas A BMC Microbiol Research Article BACKGROUND: Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples and only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled group in marine environments. Using 454 diversity ‘tag’ sequencing we investigate the diversity and distribution of these protists in marine sediments and water column samples taken from the Deep Chlorophyll Maximum (DCM) and sub-surface using both DNA and RNA as the source template and sampling four European offshore locations. RESULTS: We detected the presence of 265 sequences branching with known Perkinsea, the majority of them recovered from marine sediments. Moreover, 27% of these sequences were sampled from RNA derived cDNA libraries. Phylogenetic analyses classify a large proportion of these sequences into 38 cluster groups (including 30 novel marine cluster groups), which share less than 97% sequence similarity suggesting this diversity encompasses a range of biologically and ecologically distinct organisms. CONCLUSIONS: These results demonstrate that the Perkinsea lineage is considerably more diverse than previously detected in marine environments. This wide diversity of Perkinsea-like protists is largely retrieved in marine sediment with a significant proportion detected in RNA derived libraries suggesting this diversity represents ribosomally ‘active’ and intact cells. Given the phylogenetic range of hosts infected by known Perkinsea parasites, these data suggest that Perkinsea either play a significant but hitherto unrecognized role as parasites in marine sediments and/or members of this group are present in the marine sediment possibly as part of the ‘seed bank’ microbial community. BioMed Central 2014-04-29 /pmc/articles/PMC4044210/ /pubmed/24779375 http://dx.doi.org/10.1186/1471-2180-14-110 Text en Copyright © 2014 Chambouvet et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
spellingShingle Research Article
Chambouvet, Aurélie
Berney, Cédric
Romac, Sarah
Audic, Stéphane
Maguire, Finlay
De Vargas, Colomban
Richards, Thomas A
Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments
title Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments
title_full Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments
title_fullStr Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments
title_full_unstemmed Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments
title_short Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments
title_sort diverse molecular signatures for ribosomally ‘active’ perkinsea in marine sediments
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044210/
https://www.ncbi.nlm.nih.gov/pubmed/24779375
http://dx.doi.org/10.1186/1471-2180-14-110
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