AMT14 Pico-plankton, nano-plankton and bacteria abundance from AFC analysis of samples collected from CTD bottle samples
Originator's Protocol for Data Acquisition and Analysis
Water samples were collected and analysed live and preserved for determination of microbial concentration, biomass and composition. Fresh seawater samples were collected in acid clean 50 ml polypropylene bottles from a Seabird CTD system containing 24 x 20 L Niskin bottles from predawn and late morning (11:00 local time) and dusk opportunity CTD casts. Samples were stored in a refrigerator and analysed within 1-2 hours of collection.
Fresh samples were measured using a Becton Dickinson FACSort instrument, which characterised and enumerated Prochlorococcus spp. and Synechococcus spp. (cyanobacteria), heterotrophic bacteria and picoeukaryotes based on their light scattering and autofluorescence properties. Microorganisms were preserved with paraformaldehyde (1% final) and then stained with SYBR Green I nucleic acid stain. The samples were then left in the dark at room temperature for at least 1 hour before enumeration of bacterioplankton by a flow cytometer.
References Cited
Instrumentation Description
Becton Dickinson FACSort instrument
BODC Data Processing Procedures
Data were submitted via email in an Excel spreadsheet with additional or revised data submitted in a further 4 files. All files were archived under BODC's accession number SOC040128. Sample metadata (CTD number, latitude and depth) were checked against information held in the database. There were three discrepancies between the metadata provided and that held in the database. The submitted data file listed values for CTD 42 sampled at 180m although no bottle was fired at this depth. The data originator was contacted a confirmed the sample labeled 180m should have been labeled 190m and the subsequent sample data from successive deeper depths with the sample data from 300m being incorrect and hence deleted. The same discrepancy was noted for cast 19 where depth 163.5 should have been labeled 170m with the same knock on effect on the sampled depths and data provided as for cast 42. The data originator advised the depths provided from cast 47 contained 2 errors: the samples lablled 17m were actually from 7m and the samples from 65m were from 12m. In each case the data were loaded based on the corrected depth profiles.
The data were provided in cell abundance per millilitre. These units were consistent with the BODC parameter code units and no conversions were necessary.
The data were reformatted and loaded in BODC's samples database under Oracle Relational Database Management System. Data were marked up with BODC parameter codes and loaded into the database. Individual samples were matched through rosette sampling bottle and depth.
A parameter mapping table is provided below;
| Originator's Parameter | Units | Description | BODC Parameter Code | Units | Comments |
|---|---|---|---|---|---|
| Synechococcus spp. | cell abundance ml -1 | Abundance of Synechococcus spp. (ITIS: 773: WoRMS 160572) per unit volume of the water body by automated flow cytometry | P700A90Z | cell abundance ml -1 | n/a |
| Prochlorococcus spp. | cell abundance ml -1 | Abundance of Prochlorococcus spp. (ITIS: 610076: WoRMS 345515) per unit volume of the water body by automated flow cytometry | P701A90Z | cell abundance ml -1 | n/a |
| Pico-eukaryote phytoplankton (<2 µm) | cell abundance ml -1 | Abundance of Picoeukaryotic cells per unit volume of the water body by automated flow cytometry | PYEUA00A | cell abundance ml -1 | n/a |
| Stained bacteria | cell abundance ml -1 | Abundance of Bacteria (ITIS: 202421: WoRMS 6) per unit volume of the water body by automated flow cytometry | TBCCAFTX | cell abundance ml -1 | n/a |
| Bacteria standard deviation | cell abundance ml -1 | Abundance standard deviation of Bacteria (ITIS: 202421: WoRMS 6) per unit volume of the water body by automated flow cytometry | H396080A | cell abundance ml -1 | n/a |
Data Quality Report
BODC were not advised of specific quality checks carried out by the data originators. There were no standout values in the sample data provided to BODC.
Problem Report
Not relevant to this data set.
