AMT16 Pico-plankton, nano-plankton and bacteria abundance from AFC analysis of samples collected from CTD bottle samples during AMT16
Originator's Protocol for Data Acquisition and Analysis
This data originates from analyses on samples collected from CTD casts during the cruise. Samples were taken from the pre-dawn CTD cast (~0200 - 0400h local time) and from the late morning 'optics' cast (1100h local time).
Seawater samples were collected in HCl washed 50ml polypropylene tubes from each depth on 3am and 11am casts. Samples were stored in a refrigerator and analysed within 1-2 hours of collection.
Another set of samples were stained with Sybr Green I nucleic acid stain, with the addition of 0.5 µm beads as an internal standard and a potassium citrate buffer and left in the dark at 35 o C for at least 1 hour before analysis by flow cytometry onboard ship. The data were stored on disk and analysed back in the UK.
Additional subsamples were fixed with paraformaldehyde (1% final concentration) and flash frozen in liquid nitrogen for approximately 1 minute and then placed in the -60 o C freezer for post-cruise flow cytometric analysis of autotrophic and heterotrophic picoplankton abundance.
Fresh samples were measured using a Becton Dickinson FACSort flow cytometer, which characterised and enumerated Prochlorococcus spp. and Synechococcus spp. (both cyanobacteria), pico-eukaryotes, cryptophytes, coccolithophores and other nano-phytoplnkton based on their light scattering and autofluorescence properties.
After sample analysis, a density plot of particle light scatter vs green fluorescence, which is due to the Sybr Green I dye was plotted. The dye binds to the DNA in cells (including phytoplankton and viruses) and, the data originator advised that through experience, a protocol has been developed to specifically analyse bacteria. The density plots clearly show different clusters with different light scattering and green fluorescence properties and regions can be drawn around the different clusters and the numbers within them obtained to provide abundances for heterotrophic bacteria with low or high nucleic acid content.
A similar technique was applied to the Synechococcus spp. based on the bright/dim orange fluorescence of the phycoerythrin proteins in the cells.
The frozen samples were analysed post-cruise using flow cytometric analysis. This data was used to compare the effects of fixation, preservation and time on abundance estimates obtained by flow cytometry.
References Cited
Instrumentation Description
Becton Dickinson FACSort instrument
BODC Data Processing Procedures
Data were submitted via email in an Excel spreadsheet archived under BODC's accession number PML060508. Sample metadata in the file (lat, lon, depth, cast) were checked against information held in the database. There were no discrepancies.
There were a number of cells in the worksheet with '#VALUE!' or '#N/A' suggesting a problem with a formula or the data for these samples. The data originator clarified these cells should be treated as no data collected.
Since the data originator was unclear on the exact biological significance of the division between bright and dim orange fluorescence Synechococcus spp. abundance, these were combined to total Synechococcus spp. abundance for loading into the database. This is consistent with the Synechococcus spp. data returned from other AMT cruise. BODC retains the split data in the archived file and this can be provided if requested.
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 |
| Picoeukaryote 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 |
| Nanoeukaryote phytoplankton (approx. 2-12 µm) | cell abundance ml -1 | Abundance of nanoeukaryotic cells [Size: 2-12um] per unit volume of the water body by automated flow cytometry | X726A86B | 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 |
| Cryptophyceae | 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 |
| Heterotrophic bacteria (high nucleic acid content) | 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 | P18318A9 | cell abundance ml -1 | n/a |
| Heterotrophic bacteria (low nucleic acid content) | 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 | C804B6A6 | 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.
