Microbial community in the sediment of the arctic Smeerenburgfjorden
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| Natura: | Dataset Open Access |
| Lingua: | en |
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PANGAEA
2016
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| _version_ | 1867170063806627840 |
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| author | Ravenschlag, Katrin Sahm, Kerstin Amann, Rudolf |
| author_facet | Ravenschlag, Katrin Sahm, Kerstin Amann, Rudolf |
| collection | Datos científicos de ciencias marinas y ambientales |
| contents | 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 Open Access |
| id | pangaea_https___doi_org_10_1594_PANGAEA_858461 |
| institution | PANGAEA |
| language | en |
| publishDate | 2016 |
| publisher | PANGAEA |
| record_format | pangaea |
| spellingShingle | Microbial community in the sediment of the arctic Smeerenburgfjorden Ravenschlag, Katrin Sahm, Kerstin Amann, Rudolf Archaea, targed with ARCH915 oligonucleotide FISH-probe; Bacteria, targeted with EUB338 l oligonucleotides FISH-probe; Core; 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; Gammaproteobacteria, 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 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. |
| title | Microbial community in the sediment of the arctic Smeerenburgfjorden |
| topic | Archaea, targed with ARCH915 oligonucleotide FISH-probe; Bacteria, targeted with EUB338 l oligonucleotides FISH-probe; Core; 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; Gammaproteobacteria, 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 |
| url | https://doi.org/10.1594/PANGAEA.858461 |