Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden
The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes. Samples stored in PBS-ethanol were di...
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Format: | Dataset |
Language: | English |
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PANGAEA
2016
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Subjects: | |
Online Access: | https://doi.pangaea.de/10.1594/PANGAEA.858334 https://doi.org/10.1594/PANGAEA.858334 |
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ftpangaea:oai:pangaea.de:doi:10.1594/PANGAEA.858334 |
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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 |
Bacteria sulfate reducing targed with EUB338(I-III) oligonucleotide FISH-probe Core Date/Time of event DEPTH sediment/rock Desulfobacterium spp. targeted with 221 oligonucleotides FISH-probe Desulfobacter spp. targeted with DSB985 oligonucleotides FISH-probe Desulfobulbus spp. targeted with 660 oligonucleotides FISH-probe Desulforhopalus spp. targeted with DSR651 oligonucleotides FISH-probe Desulfotalea spp. targeted with Sval428 oligonucleotides FISH-probe Desulfovibrio spp. targeted with DSV698 oligonucleotides FISH-probe Desulfuromonas spp. targeted with DRM432 oligonucleotides FISH-probe Desulfusarcina/Desulfococcus targeted with DSS658 oligonucleotide FISH-probe Epifluorescence microscopy after DAPI staining Event label Fluorescence in situ hybridization (FISH) Latitude of event Longitude of event Prokaryotes abundance as single cells SBF_19980728 Smeerenburgfjorden Svalbard Svalbard clone group SVAL1 targeted with DSS225 oligonucleotide FISH-probe Svalbard clones Sva0081/Sva0863 targeted with cl81-644 oligonucleotide FISH-probe |
spellingShingle |
Bacteria sulfate reducing targed with EUB338(I-III) oligonucleotide FISH-probe Core Date/Time of event DEPTH sediment/rock Desulfobacterium spp. targeted with 221 oligonucleotides FISH-probe Desulfobacter spp. targeted with DSB985 oligonucleotides FISH-probe Desulfobulbus spp. targeted with 660 oligonucleotides FISH-probe Desulforhopalus spp. targeted with DSR651 oligonucleotides FISH-probe Desulfotalea spp. targeted with Sval428 oligonucleotides FISH-probe Desulfovibrio spp. targeted with DSV698 oligonucleotides FISH-probe Desulfuromonas spp. targeted with DRM432 oligonucleotides FISH-probe Desulfusarcina/Desulfococcus targeted with DSS658 oligonucleotide FISH-probe Epifluorescence microscopy after DAPI staining Event label Fluorescence in situ hybridization (FISH) Latitude of event Longitude of event Prokaryotes abundance as single cells SBF_19980728 Smeerenburgfjorden Svalbard Svalbard clone group SVAL1 targeted with DSS225 oligonucleotide FISH-probe Svalbard clones Sva0081/Sva0863 targeted with cl81-644 oligonucleotide FISH-probe Ravenschlag, Katrin Sahm, Kerstin Knoblauch, Christian Jørgensen, Bo Barker Amann, Rudolf I Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden |
topic_facet |
Bacteria sulfate reducing targed with EUB338(I-III) oligonucleotide FISH-probe Core Date/Time of event DEPTH sediment/rock Desulfobacterium spp. targeted with 221 oligonucleotides FISH-probe Desulfobacter spp. targeted with DSB985 oligonucleotides FISH-probe Desulfobulbus spp. targeted with 660 oligonucleotides FISH-probe Desulforhopalus spp. targeted with DSR651 oligonucleotides FISH-probe Desulfotalea spp. targeted with Sval428 oligonucleotides FISH-probe Desulfovibrio spp. targeted with DSV698 oligonucleotides FISH-probe Desulfuromonas spp. targeted with DRM432 oligonucleotides FISH-probe Desulfusarcina/Desulfococcus targeted with DSS658 oligonucleotide FISH-probe Epifluorescence microscopy after DAPI staining Event label Fluorescence in situ hybridization (FISH) Latitude of event Longitude of event Prokaryotes abundance as single cells SBF_19980728 Smeerenburgfjorden Svalbard Svalbard clone group SVAL1 targeted with DSS225 oligonucleotide FISH-probe Svalbard clones Sva0081/Sva0863 targeted with cl81-644 oligonucleotide FISH-probe |
description |
The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes. Samples stored in PBS-ethanol were diluted and treated by mild sonication. A 10-ml aliquot of a 1:40 dilution was filtered onto a 0.2-mm-pore-size type GTTP polycarbonate filter (Millipore, Eschborn, Germany). Hybridization and microscopic counting of hybridized and 49,69-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). Details of probes and formamide concentrations which were used are listed in futher details. Means were calculated by using 10 to 20 randomly chosen fields for each filter section, which corresponded to 800 to 1,000 DAPI-stained cells. Counting results were always corrected by subtracting signals observed with probe NON338. The SRB community was dominated by members of the Desulfosarcina-Desulfococcus group. This group accounted for up to 73% of the SRB detected. The predominance was shown to be a common feature for different stations along the coast of Svalbard. In a top-to-bottom approach we aimed to further resolve the composition of this large group of SRB by using probes for cultivated genera. While this approach failed, directed cloning of probe-targeted genes encoding 16S rRNA was successful and resulted in sequences which were all affiliated with the Desulfosarcina-Desulfococcus group. A group of clone sequences (group SVAL1) most closely related to Desulfosarcina variabilis (91.2% sequence similarity) was dominant and was shown to be most abundant in situ, accounting for up to 54.8% of the total SRB detected. |
format |
Dataset |
author |
Ravenschlag, Katrin Sahm, Kerstin Knoblauch, Christian Jørgensen, Bo Barker Amann, Rudolf I |
author_facet |
Ravenschlag, Katrin Sahm, Kerstin Knoblauch, Christian Jørgensen, Bo Barker Amann, Rudolf I |
author_sort |
Ravenschlag, Katrin |
title |
Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden |
title_short |
Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden |
title_full |
Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden |
title_fullStr |
Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden |
title_full_unstemmed |
Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden |
title_sort |
community structure of sulfate reducing bacteria in the sediment of the arctic smeerenburgfjorden |
publisher |
PANGAEA |
publishDate |
2016 |
url |
https://doi.pangaea.de/10.1594/PANGAEA.858334 https://doi.org/10.1594/PANGAEA.858334 |
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: 0.0950 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; Knoblauch, Christian; Jørgensen, Bo Barker; Amann, Rudolf I (2000): Community Structure, Cellular rRNA Content, and Activity of Sulfate-Reducing Bacteria in Marine Arctic Sediments. Applied and Environmental Microbiology, 66(8), 3592-3602, https://doi.org/10.1128/AEM.66.8.3592-3602.2000 |
op_relation |
Oligonucleotide probes and formamide concentration used in Ravenschlag et al., 2000 (URI: https://store.pangaea.de/Publications/Ravenschlag-etal_2000/Oligonucleotide-probes_Ravenschlag-etal_2000.pdf) https://doi.pangaea.de/10.1594/PANGAEA.858334 https://doi.org/10.1594/PANGAEA.858334 |
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.858334 https://doi.org/10.1128/AEM.66.8.3592-3602.2000 |
_version_ |
1766301037420871680 |
spelling |
ftpangaea:oai:pangaea.de:doi:10.1594/PANGAEA.858334 2023-05-15T14:27:21+02:00 Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden Ravenschlag, Katrin Sahm, Kerstin Knoblauch, Christian Jørgensen, Bo Barker Amann, Rudolf I 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: 0.0950 m 2016-02-24 text/tab-separated-values, 337 data points https://doi.pangaea.de/10.1594/PANGAEA.858334 https://doi.org/10.1594/PANGAEA.858334 en eng PANGAEA Oligonucleotide probes and formamide concentration used in Ravenschlag et al., 2000 (URI: https://store.pangaea.de/Publications/Ravenschlag-etal_2000/Oligonucleotide-probes_Ravenschlag-etal_2000.pdf) https://doi.pangaea.de/10.1594/PANGAEA.858334 https://doi.org/10.1594/PANGAEA.858334 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; Knoblauch, Christian; Jørgensen, Bo Barker; Amann, Rudolf I (2000): Community Structure, Cellular rRNA Content, and Activity of Sulfate-Reducing Bacteria in Marine Arctic Sediments. Applied and Environmental Microbiology, 66(8), 3592-3602, https://doi.org/10.1128/AEM.66.8.3592-3602.2000 Bacteria sulfate reducing targed with EUB338(I-III) oligonucleotide FISH-probe Core Date/Time of event DEPTH sediment/rock Desulfobacterium spp. targeted with 221 oligonucleotides FISH-probe Desulfobacter spp. targeted with DSB985 oligonucleotides FISH-probe Desulfobulbus spp. targeted with 660 oligonucleotides FISH-probe Desulforhopalus spp. targeted with DSR651 oligonucleotides FISH-probe Desulfotalea spp. targeted with Sval428 oligonucleotides FISH-probe Desulfovibrio spp. targeted with DSV698 oligonucleotides FISH-probe Desulfuromonas spp. targeted with DRM432 oligonucleotides FISH-probe Desulfusarcina/Desulfococcus targeted with DSS658 oligonucleotide FISH-probe Epifluorescence microscopy after DAPI staining Event label Fluorescence in situ hybridization (FISH) Latitude of event Longitude of event Prokaryotes abundance as single cells SBF_19980728 Smeerenburgfjorden Svalbard Svalbard clone group SVAL1 targeted with DSS225 oligonucleotide FISH-probe Svalbard clones Sva0081/Sva0863 targeted with cl81-644 oligonucleotide FISH-probe Dataset 2016 ftpangaea https://doi.org/10.1594/PANGAEA.858334 https://doi.org/10.1128/AEM.66.8.3592-3602.2000 2023-01-20T09:06:56Z The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes. Samples stored in PBS-ethanol were diluted and treated by mild sonication. A 10-ml aliquot of a 1:40 dilution was filtered onto a 0.2-mm-pore-size type GTTP polycarbonate filter (Millipore, Eschborn, Germany). Hybridization and microscopic counting of hybridized and 49,69-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). Details of probes and formamide concentrations which were used are listed in futher details. Means were calculated by using 10 to 20 randomly chosen fields for each filter section, which corresponded to 800 to 1,000 DAPI-stained cells. Counting results were always corrected by subtracting signals observed with probe NON338. The SRB community was dominated by members of the Desulfosarcina-Desulfococcus group. This group accounted for up to 73% of the SRB detected. The predominance was shown to be a common feature for different stations along the coast of Svalbard. In a top-to-bottom approach we aimed to further resolve the composition of this large group of SRB by using probes for cultivated genera. While this approach failed, directed cloning of probe-targeted genes encoding 16S rRNA was successful and resulted in sequences which were all affiliated with the Desulfosarcina-Desulfococcus group. A group of clone sequences (group SVAL1) most closely related to Desulfosarcina variabilis (91.2% sequence similarity) was dominant and was shown to be most abundant in situ, accounting for up to 54.8% of the total SRB detected. 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) |