Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden
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PANGAEA
2016
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| _version_ | 1867169110680403968 |
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| 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 |
| collection | Datos científicos de ciencias marinas y ambientales |
| contents | 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 Open Access |
| id | pangaea_https___doi_org_10_1594_PANGAEA_858334 |
| institution | PANGAEA |
| language | en |
| publishDate | 2016 |
| publisher | PANGAEA |
| record_format | pangaea |
| spellingShingle | 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 Bacteria, sulfate reducing; Bacteria, targed with EUB338(I-III) oligonucleotide FISH-probe; Core; 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 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. |
| title | Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden |
| topic | Bacteria, sulfate reducing; Bacteria, targed with EUB338(I-III) oligonucleotide FISH-probe; Core; 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 |
| url | https://doi.org/10.1594/PANGAEA.858334 |