Microbial community in the sediment of the arctic Smeerenburgfjorden, supplement to: Ravenschlag, Katrin; Sahm, Kerstin; Amann, Rudolf (2001): Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Applied and Environmental Microbiology, 67(1), 387-395
Fluorescence in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes were used to investigate the phylogenetic composition of a marine Arctic sediment (Svalbard). Hybridization and microscopy counts of hybridized and 4',6'-diamidino-2-phenylindole (DAPI)-stained cells we...
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ftdatacite:10.1594/pangaea.858461 2023-05-15T14:59:47+02:00 Microbial community in the sediment of the arctic Smeerenburgfjorden, supplement to: Ravenschlag, Katrin; Sahm, Kerstin; Amann, Rudolf (2001): Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Applied and Environmental Microbiology, 67(1), 387-395 Ravenschlag, Katrin Sahm, Kerstin Amann, Rudolf 2016 text/tab-separated-values https://dx.doi.org/10.1594/pangaea.858461 https://doi.pangaea.de/10.1594/PANGAEA.858461 en eng PANGAEA - Data Publisher for Earth & Environmental Science https://store.pangaea.de/Publications/Ravenschlag-etal_2001/Oligonucleotide-probes_Ravenschlag-etal_2001.pdf https://dx.doi.org/10.1128/aem.67.1.387-395.2001 https://store.pangaea.de/Publications/Ravenschlag-etal_2001/Oligonucleotide-probes_Ravenschlag-etal_2001.pdf Creative Commons Attribution 3.0 Unported https://creativecommons.org/licenses/by/3.0/legalcode cc-by-3.0 CC-BY Event label Latitude of event Longitude of event DEPTH, sediment/rock Prokaryotes, abundance as single cells Bacteria, targeted with EUB338 l oligonucleotides FISH-probe Archaea, targed with ARCH915 oligonucleotide FISH-probe Cytophaga-Flavobacterium cluster, targeted with CF319a oligonucleotide FISH-probe Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe Gammaproteobacteria, targeted with GAM660 oligonucleotide FISH-probe Planctomycetales, targeted with PLA886 oligonucleotide FISH-probe Core Epifluorescence microscopy after DAPI staining Fluorescence in situ hybridization FISH Dataset dataset Supplementary Dataset 2016 ftdatacite https://doi.org/10.1594/pangaea.858461 https://doi.org/10.1128/aem.67.1.387-395.2001 2022-02-09T13:17:41Z Fluorescence in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes were used to investigate the phylogenetic composition of a marine Arctic sediment (Svalbard). Hybridization and microscopy counts of hybridized and 4',6'-diamidino-2-phenylindole (DAPI)-stained cells were performed as described previously from Snaidr et al. (1997, http://aem.asm.org/content/63/7/2884.full.pdf). Means were calculated from 10 to 20 randomly chosen fields on each filter section, corresponding to 800 to 1,000 DAPI-stained cells. Counting results were always corrected by subtracting signals observed with the probe NON338. Formamide concentrations are given in further details. FISH resulted in the detection of a large fraction of microbes living in the top 5 cm of the sediment. Up to 65.4% ± 7.5% of total DAPI cell counts hybridized to the bacterial probe EUB338, and up to 4.9% ± 1.5% hybridized to the archaeal probe ARCH915. Besides delta-proteobacterial sulfate-reducing bacteria (up to 16% 52) members of the Cytophaga-Flavobacterium cluster were the most abundant group detected in this sediment, accounting for up to 12.8% of total DAPI cell counts. Furthermore, members of the order Planctomycetales accounted for up to 3.9% of total cell counts. In accordance with previous studies, these findings support the hypothesis that these bacterial groups are not simply settling with organic matter from the pelagic zone but are indigenous to the anoxic zones of marine sediments. Members of the gamma-proteobacteria also constituted a significant fraction in this sediment (6.1% ± 2.5% of total cell counts). A new probe (GAM660) specific for sequences affiliated with free-living or endosymbiotic sulfur-oxidizing bacteria was developed. A significant number of cells was detected by this probe (2.1% ± 0.7% of total DAPI cell counts), showing no clear zonation along the vertical profile. Gram-positive bacteria and the beta-proteobacteria were near the detection limit in all sediments. Dataset Arctic Smeerenburgfjord* Svalbard DataCite Metadata Store (German National Library of Science and Technology) Arctic Smeerenburgfjorden ENVELOPE(11.158,11.158,79.681,79.681) Svalbard |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
Event label Latitude of event Longitude of event DEPTH, sediment/rock Prokaryotes, abundance as single cells Bacteria, targeted with EUB338 l oligonucleotides FISH-probe Archaea, targed with ARCH915 oligonucleotide FISH-probe Cytophaga-Flavobacterium cluster, targeted with CF319a oligonucleotide FISH-probe Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe Gammaproteobacteria, targeted with GAM660 oligonucleotide FISH-probe Planctomycetales, targeted with PLA886 oligonucleotide FISH-probe Core Epifluorescence microscopy after DAPI staining Fluorescence in situ hybridization FISH |
spellingShingle |
Event label Latitude of event Longitude of event DEPTH, sediment/rock Prokaryotes, abundance as single cells Bacteria, targeted with EUB338 l oligonucleotides FISH-probe Archaea, targed with ARCH915 oligonucleotide FISH-probe Cytophaga-Flavobacterium cluster, targeted with CF319a oligonucleotide FISH-probe Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe Gammaproteobacteria, targeted with GAM660 oligonucleotide FISH-probe Planctomycetales, targeted with PLA886 oligonucleotide FISH-probe Core Epifluorescence microscopy after DAPI staining Fluorescence in situ hybridization FISH Ravenschlag, Katrin Sahm, Kerstin Amann, Rudolf Microbial community in the sediment of the arctic Smeerenburgfjorden, supplement to: Ravenschlag, Katrin; Sahm, Kerstin; Amann, Rudolf (2001): Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Applied and Environmental Microbiology, 67(1), 387-395 |
topic_facet |
Event label Latitude of event Longitude of event DEPTH, sediment/rock Prokaryotes, abundance as single cells Bacteria, targeted with EUB338 l oligonucleotides FISH-probe Archaea, targed with ARCH915 oligonucleotide FISH-probe Cytophaga-Flavobacterium cluster, targeted with CF319a oligonucleotide FISH-probe Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe Gammaproteobacteria, targeted with GAM660 oligonucleotide FISH-probe Planctomycetales, targeted with PLA886 oligonucleotide FISH-probe Core Epifluorescence microscopy after DAPI staining Fluorescence in situ hybridization FISH |
description |
Fluorescence in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes were used to investigate the phylogenetic composition of a marine Arctic sediment (Svalbard). Hybridization and microscopy counts of hybridized and 4',6'-diamidino-2-phenylindole (DAPI)-stained cells were performed as described previously from Snaidr et al. (1997, http://aem.asm.org/content/63/7/2884.full.pdf). Means were calculated from 10 to 20 randomly chosen fields on each filter section, corresponding to 800 to 1,000 DAPI-stained cells. Counting results were always corrected by subtracting signals observed with the probe NON338. Formamide concentrations are given in further details. FISH resulted in the detection of a large fraction of microbes living in the top 5 cm of the sediment. Up to 65.4% ± 7.5% of total DAPI cell counts hybridized to the bacterial probe EUB338, and up to 4.9% ± 1.5% hybridized to the archaeal probe ARCH915. Besides delta-proteobacterial sulfate-reducing bacteria (up to 16% 52) members of the Cytophaga-Flavobacterium cluster were the most abundant group detected in this sediment, accounting for up to 12.8% of total DAPI cell counts. Furthermore, members of the order Planctomycetales accounted for up to 3.9% of total cell counts. In accordance with previous studies, these findings support the hypothesis that these bacterial groups are not simply settling with organic matter from the pelagic zone but are indigenous to the anoxic zones of marine sediments. Members of the gamma-proteobacteria also constituted a significant fraction in this sediment (6.1% ± 2.5% of total cell counts). A new probe (GAM660) specific for sequences affiliated with free-living or endosymbiotic sulfur-oxidizing bacteria was developed. A significant number of cells was detected by this probe (2.1% ± 0.7% of total DAPI cell counts), showing no clear zonation along the vertical profile. Gram-positive bacteria and the beta-proteobacteria were near the detection limit in all sediments. |
format |
Dataset |
author |
Ravenschlag, Katrin Sahm, Kerstin Amann, Rudolf |
author_facet |
Ravenschlag, Katrin Sahm, Kerstin Amann, Rudolf |
author_sort |
Ravenschlag, Katrin |
title |
Microbial community in the sediment of the arctic Smeerenburgfjorden, supplement to: Ravenschlag, Katrin; Sahm, Kerstin; Amann, Rudolf (2001): Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Applied and Environmental Microbiology, 67(1), 387-395 |
title_short |
Microbial community in the sediment of the arctic Smeerenburgfjorden, supplement to: Ravenschlag, Katrin; Sahm, Kerstin; Amann, Rudolf (2001): Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Applied and Environmental Microbiology, 67(1), 387-395 |
title_full |
Microbial community in the sediment of the arctic Smeerenburgfjorden, supplement to: Ravenschlag, Katrin; Sahm, Kerstin; Amann, Rudolf (2001): Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Applied and Environmental Microbiology, 67(1), 387-395 |
title_fullStr |
Microbial community in the sediment of the arctic Smeerenburgfjorden, supplement to: Ravenschlag, Katrin; Sahm, Kerstin; Amann, Rudolf (2001): Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Applied and Environmental Microbiology, 67(1), 387-395 |
title_full_unstemmed |
Microbial community in the sediment of the arctic Smeerenburgfjorden, supplement to: Ravenschlag, Katrin; Sahm, Kerstin; Amann, Rudolf (2001): Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Applied and Environmental Microbiology, 67(1), 387-395 |
title_sort |
microbial community in the sediment of the arctic smeerenburgfjorden, supplement to: ravenschlag, katrin; sahm, kerstin; amann, rudolf (2001): quantitative molecular analysis of the microbial community in marine arctic sediments (svalbard). applied and environmental microbiology, 67(1), 387-395 |
publisher |
PANGAEA - Data Publisher for Earth & Environmental Science |
publishDate |
2016 |
url |
https://dx.doi.org/10.1594/pangaea.858461 https://doi.pangaea.de/10.1594/PANGAEA.858461 |
long_lat |
ENVELOPE(11.158,11.158,79.681,79.681) |
geographic |
Arctic Smeerenburgfjorden Svalbard |
geographic_facet |
Arctic Smeerenburgfjorden Svalbard |
genre |
Arctic Smeerenburgfjord* Svalbard |
genre_facet |
Arctic Smeerenburgfjord* Svalbard |
op_relation |
https://store.pangaea.de/Publications/Ravenschlag-etal_2001/Oligonucleotide-probes_Ravenschlag-etal_2001.pdf https://dx.doi.org/10.1128/aem.67.1.387-395.2001 https://store.pangaea.de/Publications/Ravenschlag-etal_2001/Oligonucleotide-probes_Ravenschlag-etal_2001.pdf |
op_rights |
Creative Commons Attribution 3.0 Unported https://creativecommons.org/licenses/by/3.0/legalcode cc-by-3.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1594/pangaea.858461 https://doi.org/10.1128/aem.67.1.387-395.2001 |
_version_ |
1766331903313444864 |