Microbial community in the sediment of the arctic Smeerenburgfjorden
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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Format: | Dataset |
Language: | English |
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PANGAEA
2016
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Online Access: | https://doi.pangaea.de/10.1594/PANGAEA.858461 https://doi.org/10.1594/PANGAEA.858461 |
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ftpangaea:oai:pangaea.de:doi:10.1594/PANGAEA.858461 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
PANGAEA - Data Publisher for Earth & Environmental Science |
op_collection_id |
ftpangaea |
language |
English |
topic |
Archaea targed with ARCH915 oligonucleotide FISH-probe Bacteria targeted with EUB338 l oligonucleotides FISH-probe Core Cytophaga-Flavobacterium cluster targeted with CF319a oligonucleotide FISH-probe DEPTH sediment/rock Epifluorescence microscopy after DAPI staining Event label Fluorescence in situ hybridization (FISH) Gammaproteobacteria targeted with Gam42a oligonucleotide FISH-probe targeted with GAM660 oligonucleotide FISH-probe Latitude of event Longitude of event Planctomycetales targeted with PLA886 oligonucleotide FISH-probe Prokaryotes abundance as single cells SBF_19980728 Smeerenburgfjorden Svalbard |
spellingShingle |
Archaea targed with ARCH915 oligonucleotide FISH-probe Bacteria targeted with EUB338 l oligonucleotides FISH-probe Core Cytophaga-Flavobacterium cluster targeted with CF319a oligonucleotide FISH-probe DEPTH sediment/rock Epifluorescence microscopy after DAPI staining Event label Fluorescence in situ hybridization (FISH) Gammaproteobacteria targeted with Gam42a oligonucleotide FISH-probe targeted with GAM660 oligonucleotide FISH-probe Latitude of event Longitude of event Planctomycetales targeted with PLA886 oligonucleotide FISH-probe Prokaryotes abundance as single cells SBF_19980728 Smeerenburgfjorden Svalbard Ravenschlag, Katrin Sahm, Kerstin Amann, Rudolf Microbial community in the sediment of the arctic Smeerenburgfjorden |
topic_facet |
Archaea targed with ARCH915 oligonucleotide FISH-probe Bacteria targeted with EUB338 l oligonucleotides FISH-probe Core Cytophaga-Flavobacterium cluster targeted with CF319a oligonucleotide FISH-probe DEPTH sediment/rock Epifluorescence microscopy after DAPI staining Event label Fluorescence in situ hybridization (FISH) Gammaproteobacteria targeted with Gam42a oligonucleotide FISH-probe targeted with GAM660 oligonucleotide FISH-probe Latitude of event Longitude of event Planctomycetales targeted with PLA886 oligonucleotide FISH-probe Prokaryotes abundance as single cells SBF_19980728 Smeerenburgfjorden Svalbard |
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 |
title_short |
Microbial community in the sediment of the arctic Smeerenburgfjorden |
title_full |
Microbial community in the sediment of the arctic Smeerenburgfjorden |
title_fullStr |
Microbial community in the sediment of the arctic Smeerenburgfjorden |
title_full_unstemmed |
Microbial community in the sediment of the arctic Smeerenburgfjorden |
title_sort |
microbial community in the sediment of the arctic smeerenburgfjorden |
publisher |
PANGAEA |
publishDate |
2016 |
url |
https://doi.pangaea.de/10.1594/PANGAEA.858461 https://doi.org/10.1594/PANGAEA.858461 |
op_coverage |
LATITUDE: 79.926380 * LONGITUDE: 11.135830 * DATE/TIME START: 1998-07-28T00:00:00 * DATE/TIME END: 1998-07-28T00:00:00 * MINIMUM DEPTH, sediment/rock: 0.0025 m * MAXIMUM DEPTH, sediment/rock: 0.1900 m |
long_lat |
ENVELOPE(11.158,11.158,79.681,79.681) ENVELOPE(11.135830,11.135830,79.926380,79.926380) |
geographic |
Arctic Svalbard Smeerenburgfjorden |
geographic_facet |
Arctic Svalbard Smeerenburgfjorden |
genre |
Arctic Arctic Smeerenburgfjord* Svalbard |
genre_facet |
Arctic Arctic Smeerenburgfjord* Svalbard |
op_source |
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, https://doi.org/10.1128/AEM.67.1.387-395.2001 |
op_relation |
Oligonucleotide probes and formamide concentration used in Ravenschlag et al., 2001 (URI: https://store.pangaea.de/Publications/Ravenschlag-etal_2001/Oligonucleotide-probes_Ravenschlag-etal_2001.pdf) https://doi.pangaea.de/10.1594/PANGAEA.858461 https://doi.org/10.1594/PANGAEA.858461 |
op_rights |
CC-BY-3.0: Creative Commons Attribution 3.0 Unported Access constraints: unrestricted info:eu-repo/semantics/openAccess |
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_ |
1766300583445135360 |
spelling |
ftpangaea:oai:pangaea.de:doi:10.1594/PANGAEA.858461 2023-05-15T14:27:02+02:00 Microbial community in the sediment of the arctic Smeerenburgfjorden Ravenschlag, Katrin Sahm, Kerstin Amann, Rudolf LATITUDE: 79.926380 * LONGITUDE: 11.135830 * DATE/TIME START: 1998-07-28T00:00:00 * DATE/TIME END: 1998-07-28T00:00:00 * MINIMUM DEPTH, sediment/rock: 0.0025 m * MAXIMUM DEPTH, sediment/rock: 0.1900 m 2016-02-25 text/tab-separated-values, 220 data points https://doi.pangaea.de/10.1594/PANGAEA.858461 https://doi.org/10.1594/PANGAEA.858461 en eng PANGAEA Oligonucleotide probes and formamide concentration used in Ravenschlag et al., 2001 (URI: https://store.pangaea.de/Publications/Ravenschlag-etal_2001/Oligonucleotide-probes_Ravenschlag-etal_2001.pdf) https://doi.pangaea.de/10.1594/PANGAEA.858461 https://doi.org/10.1594/PANGAEA.858461 CC-BY-3.0: Creative Commons Attribution 3.0 Unported Access constraints: unrestricted info:eu-repo/semantics/openAccess CC-BY 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, https://doi.org/10.1128/AEM.67.1.387-395.2001 Archaea targed with ARCH915 oligonucleotide FISH-probe Bacteria targeted with EUB338 l oligonucleotides FISH-probe Core Cytophaga-Flavobacterium cluster targeted with CF319a oligonucleotide FISH-probe DEPTH sediment/rock Epifluorescence microscopy after DAPI staining Event label Fluorescence in situ hybridization (FISH) Gammaproteobacteria targeted with Gam42a oligonucleotide FISH-probe targeted with GAM660 oligonucleotide FISH-probe Latitude of event Longitude of event Planctomycetales targeted with PLA886 oligonucleotide FISH-probe Prokaryotes abundance as single cells SBF_19980728 Smeerenburgfjorden Svalbard Dataset 2016 ftpangaea https://doi.org/10.1594/PANGAEA.858461 https://doi.org/10.1128/AEM.67.1.387-395.2001 2023-01-20T09:06:57Z 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 Arctic Smeerenburgfjord* Svalbard PANGAEA - Data Publisher for Earth & Environmental Science Arctic Svalbard Smeerenburgfjorden ENVELOPE(11.158,11.158,79.681,79.681) ENVELOPE(11.135830,11.135830,79.926380,79.926380) |