Metadata Report for BODC Series Reference Number 2273299

• Metadata Summary

• Problem Reports

• Data Access Policy

• Narrative Documents

• Project Information

• Data Activity or Cruise Information

• Fixed Station Information

• BODC Quality Flags

• SeaDataNet Quality Flags

Metadata Summary

Problem Reports

No Problem Report Found in the Database

Data Access Policy

Open Data

These data have no specific confidentiality restrictions for users. However, users must acknowledge data sources as it is not ethical to publish data without proper attribution. Any publication or other output resulting from usage of the data should include an acknowledgment.

If the Information Provider does not provide a specific attribution statement, or if you are using Information from several Information Providers and multiple attributions are not practical in your product or application, you may consider using the following:

"Contains public sector information licensed under the Open Government Licence v1.0."

Narrative Documents

Niskin Bottle

The Niskin bottle is a device used by oceanographers to collect subsurface seawater samples. It is a plastic bottle with caps and rubber seals at each end and is deployed with the caps held open, allowing free-flushing of the bottle as it moves through the water column.

Standard Niskin

The standard version of the bottle includes a plastic-coated metal spring or elastic cord running through the interior of the bottle that joins the two caps, and the caps are held open against the spring by plastic lanyards. When the bottle reaches the desired depth the lanyards are released by a pressure-actuated switch, command signal or messenger weight and the caps are forced shut and sealed, trapping the seawater sample.

Lever Action Niskin

The Lever Action Niskin Bottle differs from the standard version, in that the caps are held open during deployment by externally mounted stainless steel springs rather than an internal spring or cord. Lever Action Niskins are recommended for applications where a completely clear sample chamber is critical or for use in deep cold water.

Clean Sampling

A modified version of the standard Niskin bottle has been developed for clean sampling. This is teflon-coated and uses a latex cord to close the caps rather than a metal spring. The clean version of the Levered Action Niskin bottle is also teflon-coated and uses epoxy covered springs in place of the stainless steel springs. These bottles are specifically designed to minimise metal contamination when sampling trace metals.

Deployment

Bottles may be deployed singly clamped to a wire or in groups of up to 48 on a rosette. Standard bottles and Lever Action bottles have a capacity between 1.7 and 30 L. Reversing thermometers may be attached to a spring-loaded disk that rotates through 180° on bottle closure.

Bacterial abundance by flow cytometry data series for cruise Charles Darwin CD132

Content of Data Series

Originator's Protocol for Data Acquisition and Analysis

The following methodology was compiled from information extracted from the CD132 cruise report (Burkill 2002) and from methodology published in Zubkov et al (2003).

The aim was to compare abundance of dominant groups of bacterioplankton in widely different planktonic communities of the Arabian Sea. Water samples were collected and preserved for determination of bacterioplankton concentration, biomass and composition using flow cytometry and molecular methods including in situ hybridisation. Bacterioplankton metabolic activities and production were also determined on board by incubating samples with isotopically labelled precursor molecules: 3H-leucine, 14C-leucine, 3H-glucose, 14C-glucose, 33P-phosphate and 35S-methionine.

The present information relates to bacterioplankton abundance data. Vertical distributions of bacterioplankton were analysed. Concentration was determined by flow cytometry on board the ship in all collected samples. Cyanobacteria and pico-eukaryote algae were enumerated in freshly collected unstained samples using their specific chlorophyll and phycoerythrin autofluorescence (Chisholm et al 1988, Waterbury et al 1979). The abundance of total bacterioplankton was determined with a FACSort flow cytometer (Becton Dickinson, Oxford, UK) after they were stained with SYBR Green I DNA dye (Marie et al 1997). For flow cytometric analyses replicated 2ml samples were fixed with 0.75% paraformaldehyde (PFA) final concentration and stored at 2°C for 24h to enhance cell fixation. The samples were then kept at -20°C. Yellow-green beads with a 0.5µm diameter (Fluoresbrite Microparticles; Polysciences, Warrington, Pa.) were used in all analyses of fixed samples as an internal standard.

Heterotrophic bacteria abundance was calculated by subtracting the abundance of Synechococcus plus Prochlorochoccus to total bacterioplankton abundance.

References Cited

Burkill PH (2002). RRS Charles Darwin cruise 132. Analysing the Microbial Biodiversity of the Indian Ocean - AMBITION. 30 Aug-29 Sep 2001. Marine and Freshwater Microbial Biodiversity Cruise Report No.1, 56pp.

Chisholm SW, Olson RJ, Zettler ER, Goericke R, Waterbury JB, Welschmeyer NA (1988). A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334:340-343.

Marie D, Partensky F, Jacquet S, Vaulot D (1997). Enumeration and cell cycle analysis of natural populations of marine picoplankton by flow cytometry using the nucleic acid stain SYBR Green I. Appl. Environ. Microbiol. 63:186-193.

Waterbury JB, Watson SW, Guillard RRL, Brand LE (1979). Wide-spread occurrence of a unicellular, marine planktonic, cyanobacterium. Nature 277:293-294.

Zubkov MV, Fuchs BM, Tarran GA, Burkill PH, Amann R (2003). High rate of uptake of organic nitrogen compounds by Prochlorococcus cyanobacteria as a key to their dominance in oligotrophic oceanic waters. Appl. Environ. Microbiol. 69:1299-1304.

BODC Data Processing Procedures

Total bacteria and heterotrophic bacteria abundance data were submitted to BODC in a spreadsheet containing date, time, station ID, latitude, longitude and sample depth information. The data file submitted also contained cyanobacteria abundance data used by Mike Zubkov to derive heterotrophic bacteria abundances. These represented a subset of Glen Tarran's cyanobacteria abundance data (see document cd132afc_phyto) and were not therefore included in the present data set.

Total bacteria and heterotrophic bacteria abundance were assigned parameter codes defined in BODC's parameter dictionary. Sample data were then linked to sample information held in the database based on matching station ID and sampling depths, prior to loading into table BOTDATA of BODC's database.

Values from analysis on samples collected from separate Niskin bottles fired at the same depth (total bacteria abundance only) were averaged prior to loading in the database. The standard deviation of these averaged values was also loaded as a parameter in the database as an indicator of between sample variability.

Data Quality Report

The quality of the data is not affected by what follows, however users should be aware that:

• the 50m bottle from cast CD132_001 was reported as leaking by the CTD operator and has therefore been flagged 'L' in the database. However, associated data do not appear to have been affected.
• for cast CD132_034, an unplanned firing of an extra bottle at 153m was not reported in the CTD log sheet resulting in a mismatch in the attribution of bottle depth to samples collected above 200m. Samples have been re-attributed to their correct depth at BODC prior to loading in the database. The bottle entries which were affected by this problem have been associated with an 'O' flag.

Users should be aware that heterotrophic bacteria abundance values cannot always be exactly re-calculated from the abundances of total bacterioplankton minus the sum of the abundances of Synechococcus and Prochlorococcus held in the database. This is because they were calculated by the originator using measurements made on samples collected from the same Niskin sampling bottle while the data value held in BODC's database sometimes represents an average from measurements made on samples collected from different Niskin bottles fired at the same depth (see section "BODC's processing" above).

Suspect quality control flags were applied to a number of heterotrophic bacteria abundance values because the Synechococchus and Prochlorococcus abundance values which were used for the calculation were significantly different from the values provided by Glen Tarran (PML) which were already held in our database. It has not been possible to resolve these differences with the originators and the data values were therefore provisionally marked as suspect.

This affects the following samples:

• CD132_036, 45.5 and 50.9 m (no data for Synechococcus and Prochlorococcus interpreted as zero count)
• CD132_047, upper 30m (Synechococcus abundances differ)
• CD132_051, upper 80m (Synechococcus and sometimes Prochlorococcus abundances differ)
• CD132_052, upper 100m (as above)

Problem Report

None reported

Project Information

No Project Information held for the Series

Data Activity or Cruise Information

Data Activity

BODC Sample Metadata Report for CD132_CTD_CD132_023

Please note:the supplied parameters may not have been sampled from all the bottle firings described in the table above. Cross-match the Sample Reference Number above against the SAMPRFNM value in the data file to identify the relevant metadata.

Related Data Activity activities are detailed in Appendix 1

Cruise

Complete Cruise Metadata Report is available here

Fixed Station Information

No Fixed Station Information held for the Series

BODC Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

SeaDataNet Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

Appendix 1: CD132_CTD_CD132_023

Related series for this Data Activity are presented in the table below. Further information can be found by following the appropriate links.

If you are interested in these series, please be aware we offer a multiple file download service. Should your credentials be insufficient for automatic download, the service also offers a referral to our Enquiries Officer who may be able to negotiate access.