University of Hawaii, School of Ocean and Earth Science and Technology
and San Francisco State University, Tiburon Center

Tomales Bay LMER/BRIE water column biotic variables metadata file

Stephen V. Smith and James T. Hollibaugh

Map of Tomales Bay, CA





Figure 1. Map of Tomales Bay sampling stations. Most sampling was conducted between stations 0 and 18. Usually, Surface samples only were collected at stations 0, 16, and 18. Other locations were sampled at both the surface and ca. 1 meter above the bottom.

The general water sampling procedures and analytical procedures are described in Smith et al. (1987, 1989, 1991). (see reference in LMER/BRIE publications list). Subsamples for the measurements given below were taken from the same samples as the subsamples for nutrients, etc. reported in TBDISS and TBPART. Surface water samples (nominal depth 0.1 m, care taken to avoid surface film) were collected with a clean polyethylene bucket. Samples were also collected 1 m above the bottom using a 5 L Niskin water sampler. Samples were poured into 2L or 4L dark plastic HDPE bottles and placed in coolers for the trip to the laboratory. Samples were processed within 3 hr of collection.


1. STN: Station number, corresponds to the map above (Figure 1) or to distance from the mouth of the bay to the sampling location in km.

2-5. DAY, MONTH, YEAR, DOY: Day, Month, Year and Days since January 1 1987, respectively. These measurements were performed on subsamples of the samples analyzed for water chemistry and reported in TBDISS and TBPART, see those data files for additional information.

6. DEPTH: Nominal sample depth in meters.

7. CHLA: Chlorophyll concentrations in (ug/L, determined as follows. Particulate material collected on a 25 mm diameter glass fiber filter (Whatman GF/F) was extracted with 90% acetone prior to June 29, 1991 or with a mixture of acetone, dimethylsulfoxide, water and diethylamine (45:45:10:0.1 by volume, K.L. Webb pers. comm.) after June 29, 1991. Extract fluorescence was measured with a Turner Designs Model 10 fluorometer. Fluorescence was converted to chlorophyll concentration using a standard curve prepared with pure chlorophyll a (Sigma) and the volume filtered.

8 and 9. LEU1, LEU2: Incorporation rate of L-leucine in pmoles/L/hr, determined essentially as described in Hollibaugh and Wong (1992). Duplicate 5 mL subsamples were pipetted into sterile, snap-cap polypropylene culture tubes then 4,5-3H-L-leucine (NEN, 20 Ci/mmol) was added (10 nM final concentration) and the sample was mixed by gently inverting the capped tube twice. The tubes were incubated for ca. 1 hr in indirect light in water bath with the temperature set to within 3 oC of the in situ temperature. At the end of the incubation period, the sample was mixed by inverting then filtered through a 0.45 Ám pore size Millipore filter at low vacuum (<20 kPa). The filter was rinsed with unlabeled sample, extracted with iced 5% TCA and iced 80% ethanol and radioassayed using a Beckman 3801 Liquid Scintillation Counter.

10. NUMBERS: Bacterioplankton abundance in millions of cells/mL, determined as follows. Samples were preserved with 2% final concentration borate buffered formaldehyde. Bacteria were enumerated within 2 weeks of sample collection by epifluorescence microscopy after staining with DAPI (Porter and Feig 1980). Abundance can be converted to biomass using the conversion factor of 20 fgC/cell (Lee and Fuhrman 1986). The dimensions of cells in some of our samples were measured using an ocular micrometer or calibrated photographs. These measurements indicated that this biovolume-based conversion factor was appropriate for these samples. We also used size fractionation to verify this conversion factor (Hollibaugh et al. 1991).


Hollibaugh, J.T., R.W. Buddemeier and S.V. Smith. 1991. Contributions of colloidal and high molecular weight dissolved material to alkalinity and nutrient concentrations in shallow marine and estuarine systems. Mar. Chem. 33: 1-27).

Hollibaugh, J. T., and P. S. Wong, Ethanol extractable substrate pools and the incorporation of thymidine, L-leucine and other substrates by bacterioplankton, Canadian Journal of Microbiology, 38, 605-613, 1992.

Lee, S., and J. A. Fuhrman, Relationships between biovolume and biomass of naturally derived marine bacterioplankton, Applied and Environmental Microbiology, 53, 1298-1303, 1986.

Porter, K. G., and Y. S. Feig, The use of DAPI for identifying and counting aquatic microflora, Limnology and Oceanography, 25, 943-948, 1980.

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