Abundance of microbial bacteria and phytoplankton through the water column by analytical flow cytometry (AFC) analysis of samples collected from CTD casts during AMT13 (JR20030910/JR91).
Originator's Protocol for Data Acquisition and Analysis
Water samples were collected and split, one set to be analysed live and the other 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 flow cytometer
BODC Data Processing Procedures
Data were submitted via email in an Excel spreadsheet and archived under BODC's accession number PML110198. Sample metadata (Station, CTD cast, latitude, longitude, water depth, rosette bottle number and sample depth) were checked against information held in the database. Individual samples were matched through rosette sampling bottle and depth. There were three discrepancies - casts 40 and 68 were provided with samples at depths where no bottles had been fired according to the SeaBird bottle firing files. These data were loaded using the closest depths where a bottle was fired to that in the originators file. This meant, for cast 40 a bottle was fired at 80 m not 100 m, and for cast 68, bottles were fired at 79.5 m and 103.8 m not 100 m and 200 m respectively.
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.
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 |
Cryptophytes | cell abundance ml -1 | Abundance of Cryptophyceae (ITIS: 10598: WoRMS 17639) per unit volume of the water body by automated flow cytometry | J79A0596 | cell abundance ml -1 | n/a |
Coccolithophores | cell abundance ml -1 | Abundance of Coccosphaerales (ITIS: 610061: WoRMS 115059) [Subgroup: coccolithophore] per unit volume of the water body by automated flow cytometry | P490A00Z | cell abundance ml -1 | n/a |
Nanoeukaryote phytoplankton (approx. 2-12 µm) | cell abundance ml -1 | Abundance of nanoeukaryotic cells [Size: 2-12 µm] per unit volume of the water body by automated flow cytometry | X726A86B | cell abundance ml -1 | n/a |
Abundance of heterotrophic bacteria | cell abundance ml -1 | Abundance of bacteria (ITIS: 202421: WoRMS 6) [Subgroup: heterotrophic] per unit volume of the water body by flow cytometry and subtraction of Synechococcus+Prochlorococcus from total bacteria | HBCCAFTX | cell abundance ml -1 | n/a |
Abundance of total bacteria including Synechococcus and Prochlorococcus | cell abundance ml -1 | Abundance of bacteria (ITIS: 202421: WoRMS 6) per unit volume of the water body by flow cytometry | TBCCAFTX | cell abundance ml -1 | n/a |
Data Quality Report
BODC were not advised of specific quality checks carried out by the data originators.
Problem Report
Not relevant to this data set.