Processing notes compiled by Hugh Ducklow and Bob Daniels
Version 2.0 January 2005

Background and Introduction

This synthesized data set collects and summarizes in one file observations of heterotrophic bacterial biomass and production rates made during the US JGOFS Process Studies, 1989-1997. It contains estimates of integrated bacterial biomass (mmol C m^-2) and production rates (mmol C m^-2 d^-1) in carbon units for direct comparison with other related quantities (plankton biomass, primary production rates, etc). The file also includes station and sample information (date, time, event number, position).

Data were integrated to standard depths (50, 100, 200 meters) and to the local euphotic zone depth to provide a basis for comparison of stocks and water column production rates across sites and seasons.

The raw data from which these estimates were synthesized are accessible through the US JGOFS Database

Methods

Bacterial biomass is derived from measurements of bacterial abundance while production rates are derived from rates of radioisotopically-labelled precursor incorporation (Ducklow, 2000). Over the course of US JGOFS the same approach was followed but the actual protocols used evolved as new instrumentation became available. The methods used for each of the Process Studies are referenced in Table 1.

Table 1. US JGOFS Process Studies. Heterotrophic bacterioplankton sampling and measurement protocols.

In general, bacterial abundance (cells liter^-1) was determined by epifluorescence microscopy (Hobbie et al., 1977) (later in concert with video image analysis to count the cells) and then by flow cytometry (Landry et al., 1996). Abundances were converted to biomass using a single, cell-based carbon conversion factor of 15 fgC cell^-1 (1 fg = 10^-15 g). Production rates were derived from rates of ³H-leucine incorporation (pmol l^-1 hr^-1; 1 pmol = 10^-12 mole) into TCA-insoluble residues (Simon and Azam, 1989) using a conversion factor of 1.5 kgC mole^-1 leucine incorporated (Ducklow et al., 2000).

Data reduction and analysis

Sampling in all process studies yielded 6 to 12 discrete depth estimates of bacterioplankton abundance and leucine incorporation rates in the upper 100 to 200 m for each station. Bacterioplankton data are given as discrete depth listings in the US JGOFS Database in raw data units for abundance and leucine incorporation. For the analyses given here, abundances and incorporation rates for the cardinal depths of 50, 100 and 200 were obtained by linear interpolation between measured values. Euphotic zone depths were taken by consulting the C14 primary productivity listings and selecting the depth of the deepest measurement or the 1% light level if available. At stations where these measurements were not available, the euphotic zone flag was set to 0, indicating that the euphotic zone depth was unknown. At stations with a euphotic zone depth estimate, the bacteria production and biomass were reported for that depth and the euphotic zone flag was set to 1. The 'euph_zone' parameter in the dataset is simply a flag indicating whether or not a euphotic zone measurement is reported for that station.

The bacterioplankton abundance and leucine incorporation values for the base of the euphotic zone were obtained by linear interpolation between measured values. All discrete values were converted to Carbon mass units as described above. Finally, the resulting discrete, volumetric biomass and production rates were integrated using common trapezoidal integration. If sampling did not extend to one or more of the cardinal depths at a given station, linear interpolation and integration were not extended to those depths.

An example of the resulting data listing is given in Table 2. The values at cardinal depths were extracted for the final data listing. Worksheets including complete listings of all discrete measurements and calculations are available from H. Ducklow.

Table 2. Example worksheet showing measured and calculated bacterial estimates. Values were interpolated for the rows given in bold. The euphotic zone depth is 65 m (interpolated). The entries at 0 m were added assuming a well-mixed water column.

Ducklow, H. W. 2000. Bacterioplankton production and biomass in the oceans. In Microbial Ecology of the Oceans. D. L. Kirchman. ed. Wiley. New York. pp. 85-120.

Ducklow, H. W., C. Carlson, M. Church, D. Kirchman, D. Smith and G. Steward. 2001a. The seasonal development of the bacterioplankton bloom in the Ross Sea, Antarctica, 1994-1997. Deep-Sea Research II, 48, 4199-4221.

Ducklow, H. W., M. L. Dickson, D. L. Kirchman, G. Steward, J. Orchardo, J. Marra and F. Azam. 2000. Constraining bacterial production, conversion efficiency and respiration in the Ross Sea, Antarctica, January-February, 1997. Deep-Sea Research II, 47, 3227-3247.

Ducklow, H. W., D. L. Kirchman, H. L. Quinby, C. A. Carlson and H. G. Dam. 1993. Stocks and dynamics of bacterioplankton carbon during the spring bloom in the eastern North Atlantic Ocean. Deep Sea Research Part II: Topical Studies in Oceanography, 40, 245-263.

Ducklow, H. W., H. L. Quinby and C. A. Carlson. 1995. Bacterioplankton dynamics in the equatorial Pacific during the 1992 El Nino. Deep Sea Research II, 42, 621-638.

Ducklow, H. W., D. C. Smith, L. Campbell, M. R. Landry, H. L. Quinby, G. F. Steward and F. Azam. 2001b. Heterotrophic bacterioplankton in the Arabian Sea: Basinwide response to year-round high primary productivity. Deep-Sea Research (Part 2, Topical Studies in Oceanography), 48, 1303-1323.

Hobbie, J. E., R. J. Daley and S. Jasper. 1977. Use of nucleopore filters for counting bacteria by epifluorescence microscopy. Applied and Environmental Microbiology, 33, 1225-1228.

Kirchman, D. L., J. H. Rich and R. T. Barber. 1995. Biomass and biomass production of heterotrophic bacteria along 140W in the equatorial Pacific: Effect of temperature on the microbial loop. Deep Sea Research Part II: Topical Studies in Oceanography, 42, 603-619.

Landry, M. R., J. Kirshtein and J. Constantinou. 1996. Abundances and distributions of picoplankton populations in the Central Equatorial Pacific from 12 degree N to 12 degree S, 140 degree W. Deep-Sea Research II, 43, 871-890.

Simon, M. and F. Azam. 1989. Protein content and protein synthesis rates of planktonic marine bacteria. Marine Ecology Progress Series, 51, 201-213.

Hugh Ducklow

Bob Daniels