Not logged in
PANGAEA.
Data Publisher for Earth & Environmental Science

Glöckner, Frank Oliver; Fuchs, Bernhard M; Amann, Rudolf I (2016): Microbial community composition in fresh water at different stations. PANGAEA, https://doi.pangaea.de/10.1594/PANGAEA.860585 (unpublished dataset), Supplement to: Glöckner, FO et al. (1999): Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Applied and Environmental Microbiology, 65(8), 3721-3726

Show MapGoogle Earth

Abstract:
Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes was used to investigate the phylogenetic composition of bacterioplankton communities in several freshwater and marine samples. An average of about 50% of the cells were detected by probes for the domains Bacteria and Archaea. Cells were concentrated from water samples (1 to 100 ml) on white polycarbonate filters (diameter, 47 mm; pore size, 0.2 mm; type GTTP 4700 [Millipore, Eschborn, Germany]) by applying a vacuum of <25 kPa. They were subsequently fixed by covering the filter with 3 ml of a freshly prepared, phosphate-buffered saline (pH 7.2)-4% paraformaldehyde (Sigma, Deisenhofen, Germany) solution for 30 min at room temperature. Airdried filters are ready for hybridization and can be stored at 220°C or room temperature for several months without showing apparent changes. Probes BET42a, GAM42a, and PLA886 were used with competitor oligonucleotides as described previously amongst others in Manz et al., (1992; doi:10.1016/S0723-2020(11)80121-9). The filters were transferred to a vial containing 50 ml of prewarmed (48°C) washing solution (70 mM NaCl, 20 mM Tris-HCl [pH 7.4], 5 mM EDTA, 0.01% sodium dodecyl sulfate) and incubated freely floating without shaking at 48°C for 15 min. The filter sections were dried on Whatman 3M paper (Whatman Ltd., Maidstone, United Kingdom) and covered with 50 ml of DAPI solution (1 mg/ml in distilled water filtered through at 0.2-mm filter) for 5 min at room temperature in the dark. For each sample and probe, more than 500 cells were enumerated; for the DAPI examination, more than 1,500 cells were counted per sample. All probe-specific cell counts are presented as the percentage of cells visualized by DAPI. The mean abundances and standard deviations were calculated from the counts of 10 to 20 randomly chosen fields on each filter section. All counts were corrected by subtracting the counts obtained with the negative control NON338. Mean and standard deviation were calculated from the counts of 10 to 20 randomly chosen fields on each filter section.
Coverage:
Median Latitude: 5.552404 * Median Longitude: 5.817408 * South-bound Latitude: -68.842833 * West-bound Longitude: -118.448436 * North-bound Latitude: 54.188330 * East-bound Longitude: 108.164990
Date/Time Start: 1995-08-15T00:00:00 * Date/Time End: 1997-12-31T23:59:00
Minimum DEPTH, water: 0.0 m * Maximum DEPTH, water: 1455.0 m
Event(s):
AntarcticOcean-1 * Latitude: -68.842833 * Longitude: 6.018000 * Date/Time: 1996-01-15T00:00:00 * Location: Antarctic Ocean * Method/Device: Water sample (WS) * Comment: Sampling date is estimated.
AntarcticOcean-2 * Latitude: -58.942000 * Longitude: 3.974000 * Date/Time: 1996-01-15T00:00:00 * Location: Antarctic Ocean * Method/Device: Water sample (WS) * Comment: Sampling date is estimated.
AntarcticOcean-3 * Latitude: -49.490000 * Longitude: 11.393000 * Date/Time: 1996-01-15T00:00:00 * Location: Antarctic Ocean * Method/Device: Water sample (WS) * Comment: Sampling date is estimated.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Event labelEventGlöckner, Frank Oliver
2Sample commentSample commentGlöckner, Frank Oliver
3DEPTH, waterDepth watermGlöckner, Frank OliverGeocode
4Prokaryotes, number of cellProk cell abund109 #/mlGlöckner, Frank OliverEpifluorescence microscopy after DAPI stainingoriginal unit = 10**6 cells/ml
5Standard deviationStd dev±Glöckner, Frank OliverEpifluorescence microscopy after DAPI stainingoriginal unit = 10**6 cells/ml
6Bacteria, targeted with EUB338 l oligonucleotides FISH-probeEUB338 I%Glöckner, Frank OliverFluorescence in situ hybridization (FISH)
7Standard deviationStd dev±Glöckner, Frank OliverFluorescence in situ hybridization (FISH)of Bacteria, targed with EUB338-l oligonucleotides FISH-probe
8Alphaproteobacteria, targeted with ALF968 oligonucleotides FISH-probeALF968%Glöckner, Frank OliverFluorescence in situ hybridization (FISH)
9Standard deviationStd dev±Glöckner, Frank OliverFluorescence in situ hybridization (FISH)of Alphaproteobacteria, targed with ALF968 oligonucleotides FISH-probe
10Betaproteobacteria, targeted with BET42a oligonucleotides FISH-probeBET42a%Glöckner, Frank OliverFluorescence in situ hybridization (FISH)
11Standard deviationStd dev±Glöckner, Frank OliverFluorescence in situ hybridization (FISH)of Betaproteobacteria, targed with BET42a oligonucleotides FISH-probe
12Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probeGam42a%Glöckner, Frank OliverFluorescence in situ hybridization (FISH)
13Standard deviationStd dev±Glöckner, Frank OliverFluorescence in situ hybridization (FISH)of Gamma-Proteobacteria, targed with Gam42a oligonucleotide FISH-probe
14Bacteroidetes, targeted with CF319a oligonucleotide FISH-probeCF319a%Glöckner, Frank OliverFluorescence in situ hybridization (FISH)
15Standard deviationStd dev±Glöckner, Frank OliverFluorescence in situ hybridization (FISH)of Bacteroidetes, targed with CF319a oligonucleotide FISH-probe
16Planctomycetales, targeted with PLA886 oligonucleotide FISH-probePLA886%Glöckner, Frank OliverFluorescence in situ hybridization (FISH)
17Standard deviationStd dev±Glöckner, Frank OliverFluorescence in situ hybridization (FISH)of Planctomycetales, targed with PLA886 oligonucleotide FISH-probe
18Non-bacteria control, targeted with NON338 oligonucleotides FISH-probeNON338%Glöckner, Frank OliverFluorescence in situ hybridization (FISH)
19Standard deviationStd dev±Glöckner, Frank OliverFluorescence in situ hybridization (FISH)of Non-bacteria control, targed with NON338 oligonucleotides FISH-probe
Size:
401 data points

Download Data (login required)

Download dataset as tab-delimited text — use the following character encoding:

View dataset as HTML