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contact PIs:Data Object biogeochemistry microbiology
| name | title |
|---|---|
| Laura Lorenzoni | Contact |
| Dr Mary Scranton | Co-Principal Investigator |
| Dr Gordon T. Taylor | Co-Principal Investigator |
Biogeochemistry and microbiology measurements in the Cariaco Basin
Microbiology sampling is conducted during special CARIACO cruises (distinct from the monthly, core sampling, time-series cruises). The specialized microbiology cruises are usually during May and November, and can be opportunistic or process-driven. There are typically at least 2 cruises per year, during which different variables are sampled and at different depths from the standard monthly CARIACO cruises. Bacteria production data are also reported for the microbiology cruises.
Ocean time series samples are collected in standard 8L Niskin bottles. For samples in and below the oxycline, a nitrogen line is attached to the upper air vent to prevent air from entering the bottle during subsampling. Samples for live analysis are first transferred without headspace to a 1L glass sample bottle with Teflon standard taper stopper. In the ship's lab, subsamples are transferred to 25 or 40 ml incubation vials, also under nitrogen. All vials are filled from the bottom with overflow of about 3 vial volumes and then sealed with no headspace.
Low molecular weight fatty acids: Volatile fatty acids are measured using the technique developed by Yang (1991), Yang et al. (1993) and Wu and Scranton (1994). Detection limits are about 1 (M for acetate). However, in some cases, deep water values are lower than 1 micromolar for acetate in which case we have estimated blanks in individual files. Samples are poisoned with 1 ml 10N KOH per liter.
Fatty acid uptake rate constants: Acetate uptake rate constants are determined using radiolabeled tracers as described by Wu and Scranton (1994). Incubations are done anoxically in the dark in screw-top septum vials. Uptake includes both conversion of isotope to CO2 (respiration) and to biomass which can be filtered onto a 0.2 m Nuclepore filter (incorporation).
CH4 is assayed by gas chromatography using the vial equilibration technique of Johnson et al. (1990) and a Carle 211AC gas chromatograph. Samples are poisoned by addition of 10N KOH solution at a rate of 200 l per 50 ml vial.
Samples for sulfide analysis are taken in well-flushed glass syringes without bubbles and are injected into vials containing Zn-acetate. Upon return to the laboratory, the ZnS is dissolved and is analyzed spectrophotometrically by the method of Cline (1969).
Abundances of remineralizers (bacteria) and regenerators (protozoa) are determined using microscopic censuses. Preserved samples (2% formaldehyde) are stained with a fluorochrome (DAPI or acridine orange) and captured on the appropriate porosity Nuclepore membrane (0.2 or 0.8 m). Filter-retained cells are enumerated and sized by epifluorescence microscopy according to Taylor et al. (1986). Larger, less abundant protozoa are enumerated on settled samples using inverted microscopy. Abundance and distribution of methanogens are determined by an autofluorescence microscopic technique whereby the fluorescence of coenzymes F420 and F350 in cells produced by two sets of excitation and barrier filters is considered presumptive identification of methanogens (Doddema and Vogels 1978).
Bacterial incorporation is measured using 3H-leucine incorporation as described by Kirchman (1993). Triplicate samples are incubated for 10-12 h in gas-tight screw-top vials to minimized alteration of the redox potential. Time course experiments have confirmed that uptake is linear for at least 15 hours. Due to the fact that some important anaerobic bacteria appear to not take up exogenous thymidine under anoxic conditions (McDonough et al. 1986; Gilmour et al. 1990), the more common method of Fuhrman and Azam (1982) is inappropriate for this system.
17 July 2009: Prepared for OCB data system by Terry McKee (BCO-DMO, WHOI)
Data were submitted to BCO-DMO in two forms: as Microsoft Excel™ spreadsheets and as ASCII text files produced for National Oceanographic and Data Center (NODC). A separate spreadsheet and text file existed for each cruise.
Data from twenty four cruises executed between November, 1995 and November 2006 were submitted. While the cruise numbers match cruise numbers for other CARIACO time-series data, the dates are not identical. Biogeochemical measurements included Hydrogen Sulfide, Methane, elemental sulfur, Sulfite, and Thiosulfate. Microbiological measurements included total bacterial abundance, Leucine incorporation rate, total abundance of cyanobacteria, total abundance of flagellates, total abundance of ciliates, concentration of acetate, concentration of propionate, total abundance of methanogens, uptake rate constant for incorporation, uptake rate constant for respiration, total uptake rate, and dark inorganic carbon cssimilation rate. Calculations of standard deviations were included for some of the measurements. Not all cruises included all measurements, so these appear as nd (missing data) in the listings.
Since the submitted files were frequently one-of-a-kind with regard to the naming, order, and contents of the measurements, significant effort was required to prepare the data for inclusion in the OCB database. This was performed using unix shell scripts and PERL scripts. Original files were manually edited as necessary to provide the computer program with consistent input. This editing was relatively minor, but critical to processing them as a unit. The original files for each cruise were split into two parts -- microbiology in one, biogeochemistry in the other, then re-merged by cast number and depth. Missing depths were padded and, if necessary, records were sorted to increasing depths.
"low" "bad" and "b.d." were changed to "bd"
"n.s." was changed to nd
"lost" changed to nd
Cruise 112
n.g. in Thiosulfate "data contaminated." changed to nd
n.g. in CH4 data changed to nd
Cruise 108:
nd was inserted in fields where corrected depth was not provided.
nd was inserted in blank fields in Cast 2 at Depth 20 in
fields for Total Bacteria and Total Bacteria_sd
"lost" appears in 32,54,60,66,89,96
In 54,60,66, this is explained as
54: lost: all isotope recovered as CO2. Apparently acetate
in vials fully hydrolyzed before processing took place.
60: lost: all isotope recovered as CO2. Apparently acetate
in vials fully hydrolyzed before processing took place.
66: lost: blocked needle so no isotope added to vial.
n.s. appears in 54, 66, 74. in acetate and is explained as:
54: n.s. = correlation coefficient for slope of acetate
uptake <0.8; therefore rate not significant
66: n.s.: Trend in uptake (respiration or incorporation)
indeterminate or near zero. Therefore no rate
constant could be determined.
74: n.s.: Rate not significant. Correlation coefficient
(r) for line < 0.7.
The original comments in the contributed data files have been preserved in a separate file:
COMMENTS text file
| B/O Hermano Gines HG93_CARIACO |
This document is created from the content of the BCO-DMO metadata database. 2009-11-22 09:22:05
info app: /home/ocb/dbase v.090827 CLC