AMT13 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 clean 250 ml polycarbonate bottles from a Seabird CTD system containing 24 x 20 L Niskin bottles from predawn and late morning (11:00 local time) 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) 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 heterotrophic bacteria by a flow cytometer.
References Cited
Instrumentation Description
Becton Dickinson FACSort instrument
BODC Data Processing Procedures
Data were submitted via email in two Excel spreadsheets archived under BODC's accession number SOC040143. One spreadsheet contained the first submission of data, the second contained updated Prochlorococcus spp. and picoeukaryote abundances from casts 74 and 76. 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 Synechococcus spp., Prochlorococcus spp. and picoeukaryote abundances for CTD 57, with heterotrophic bacteria abundances from CTD 56. Since depths sampled and latitude in both cases were for cast 56, all data were loaded into the database against this CTD cast. The depths provided for cast 40 had a sample for 100m, however no bottle was fired at this depth according to the SeaBird bottle firing log file. The data were loaded against 80m, where a bottle was fired. The submitted data for cast 68 followed the expected profile rather than the actual profile which was affected by misfiring of bottle 24. Bottle number 24 was originally closed at 304m and then firing was also attempted for the same bottle at 205m and then at 79m. Bottle 23 was then fired at 104 metres instead of the requested 200m and bottle 22 was fired at 78m instead of the requested 100m. The rest of the sampling was completed as expected. Data were loaded based on the corrected depth profile.
Values were altered for Prochlorococcus spp. and picoeukaryote abundance counts for samples from CTD casts 74 and 76, after a corrected version was received from Jane Heywood.
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 |
Heterotrophic bacteria | cell abundance ml -1 | Abundance of Bacteria (ITIS: 202421: WoRMS 6) [Subgroup: heterotrophic] per unit volume of the water body by automated flow cytometry and subtraction of Synechococcus+Prochlorococcus from total bacteria | HBCCAFTX | 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.