Comparison between MICRO–CARD–FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic
We collected surface- and deep-water samples (maximum depth 300 m) during the spring–summer transition in the coastal Arctic along a transect in the Kongsfjorden (Ny-Ålesund, Spitsbergen, Norway) to determine the structure of the active versus total marine bacterioplankton community using different...
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ftpubmed:oai:pubmedcentral.nih.gov:3615173 2023-05-15T15:00:41+02:00 Comparison between MICRO–CARD–FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic De Corte, Daniele Sintes, Eva Yokokawa, Taichi Herndl, Gerhard J 2013-04 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3615173 http://www.ncbi.nlm.nih.gov/pubmed/23565124 https://doi.org/10.1111/1758-2229.12013 en eng Blackwell Publishing Ltd http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3615173 http://www.ncbi.nlm.nih.gov/pubmed/23565124 http://dx.doi.org/10.1111/1758-2229.12013 Copyright © 2013 Society for Applied MicrobiologyandBlackwell Publishing Ltd http://creativecommons.org/licenses/by/2.5/ Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation. CC-BY Brief Reports Text 2013 ftpubmed https://doi.org/10.1111/1758-2229.12013 2013-09-04T21:57:46Z We collected surface- and deep-water samples (maximum depth 300 m) during the spring–summer transition in the coastal Arctic along a transect in the Kongsfjorden (Ny-Ålesund, Spitsbergen, Norway) to determine the structure of the active versus total marine bacterioplankton community using different approaches. Catalysed reporter deposition–fluorescence in situ hybridization combined with microautoradiography (MICRO–CARD–FISH) was used to determine the abundance and activity of different bacterial groups. The bacterial communities were dominated by members of Alphaproteobacteria followed by Bacteroidetes, whereas Gammaproteobacteria were present at low abundance but exhibited a high percentage of active cells taking up leucine. The clone libraries of 16S rRNA genes (16S rDNA) and 16S rRNA from two different depths were used to decipher the bacterial community structure. Independently of the type of clone libraries analysed (16S rDNA- or 16S rRNA-based), four major and four minor taxonomic groups were detected. The bacterioplankton community was mainly dominated at both the DNA and the RNA levels by Alphaproteobacteria followed by Gammaproteobacteria. The Rhodobacteriaceae were the most abundant members of the Alphaproteobacteria in both DNA and RNA clone libraries, followed by the SAR11 clade, which was only detectable at the 16S rDNA level. Moreover, there was a general agreement between the results obtained with both techniques, although some specific phylogenetic groups, such as SAR11 and Roseobacter, deviated substantially from this relation. These discrepancies are most likely linked to different physiological states among members of the bacterioplankton community. Combined, MICRO–CARD–FISH and DNA and RNA clone libraries, however, allowed for accurately quantifying different bacterial groups and their activity as well as a detailed phylogenetic insight into the fractions of present versus metabolically active bacterial groups. Text Arctic Kongsfjord* Kongsfjorden Ny Ålesund Ny-Ålesund Spitsbergen PubMed Central (PMC) Arctic Norway Ny-Ålesund Environmental Microbiology Reports 5 2 272 281 |
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ftpubmed |
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English |
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Brief Reports |
spellingShingle |
Brief Reports De Corte, Daniele Sintes, Eva Yokokawa, Taichi Herndl, Gerhard J Comparison between MICRO–CARD–FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic |
topic_facet |
Brief Reports |
description |
We collected surface- and deep-water samples (maximum depth 300 m) during the spring–summer transition in the coastal Arctic along a transect in the Kongsfjorden (Ny-Ålesund, Spitsbergen, Norway) to determine the structure of the active versus total marine bacterioplankton community using different approaches. Catalysed reporter deposition–fluorescence in situ hybridization combined with microautoradiography (MICRO–CARD–FISH) was used to determine the abundance and activity of different bacterial groups. The bacterial communities were dominated by members of Alphaproteobacteria followed by Bacteroidetes, whereas Gammaproteobacteria were present at low abundance but exhibited a high percentage of active cells taking up leucine. The clone libraries of 16S rRNA genes (16S rDNA) and 16S rRNA from two different depths were used to decipher the bacterial community structure. Independently of the type of clone libraries analysed (16S rDNA- or 16S rRNA-based), four major and four minor taxonomic groups were detected. The bacterioplankton community was mainly dominated at both the DNA and the RNA levels by Alphaproteobacteria followed by Gammaproteobacteria. The Rhodobacteriaceae were the most abundant members of the Alphaproteobacteria in both DNA and RNA clone libraries, followed by the SAR11 clade, which was only detectable at the 16S rDNA level. Moreover, there was a general agreement between the results obtained with both techniques, although some specific phylogenetic groups, such as SAR11 and Roseobacter, deviated substantially from this relation. These discrepancies are most likely linked to different physiological states among members of the bacterioplankton community. Combined, MICRO–CARD–FISH and DNA and RNA clone libraries, however, allowed for accurately quantifying different bacterial groups and their activity as well as a detailed phylogenetic insight into the fractions of present versus metabolically active bacterial groups. |
format |
Text |
author |
De Corte, Daniele Sintes, Eva Yokokawa, Taichi Herndl, Gerhard J |
author_facet |
De Corte, Daniele Sintes, Eva Yokokawa, Taichi Herndl, Gerhard J |
author_sort |
De Corte, Daniele |
title |
Comparison between MICRO–CARD–FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic |
title_short |
Comparison between MICRO–CARD–FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic |
title_full |
Comparison between MICRO–CARD–FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic |
title_fullStr |
Comparison between MICRO–CARD–FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic |
title_full_unstemmed |
Comparison between MICRO–CARD–FISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic |
title_sort |
comparison between micro–card–fish and 16s rrna gene clone libraries to assess the active versus total bacterial community in the coastal arctic |
publisher |
Blackwell Publishing Ltd |
publishDate |
2013 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3615173 http://www.ncbi.nlm.nih.gov/pubmed/23565124 https://doi.org/10.1111/1758-2229.12013 |
geographic |
Arctic Norway Ny-Ålesund |
geographic_facet |
Arctic Norway Ny-Ålesund |
genre |
Arctic Kongsfjord* Kongsfjorden Ny Ålesund Ny-Ålesund Spitsbergen |
genre_facet |
Arctic Kongsfjord* Kongsfjorden Ny Ålesund Ny-Ålesund Spitsbergen |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3615173 http://www.ncbi.nlm.nih.gov/pubmed/23565124 http://dx.doi.org/10.1111/1758-2229.12013 |
op_rights |
Copyright © 2013 Society for Applied MicrobiologyandBlackwell Publishing Ltd http://creativecommons.org/licenses/by/2.5/ Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1111/1758-2229.12013 |
container_title |
Environmental Microbiology Reports |
container_volume |
5 |
container_issue |
2 |
container_start_page |
272 |
op_container_end_page |
281 |
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1766332757162590208 |