**2. Methods and materials**

## **2.1 Bioluminescence measurements**

Two defined excitation moored bathyphotometers (MOORDEX, University of California, Santa Barbara) were used in San Diego Bay (SDB) and at San Clemente Island (SCI). Under control of on-board computers, these measured stimulated bioluminescence, flow rate, and seawater temperature hourly. Every hour, seawater was pumped for 120 sec at 7-8 L sec-1 for a total volume of approximately 840 - 960 L of seawater through a darkened cylindrical 5 l detection chamber approximately 406 mm long and 127 mm in diameter (Case et al. 1993, Neilson et al. 1995). Bioluminescence, excited by the chamber spanning input impeller, was measured by a PMT receiving light from 46 fiber optics tips lining the chamber wall and expressed as photons sec-1 ml-1 of seawater.

On monthly transits between SDB and SCI an "on-board" sensor system sampled seawater continuously from 3m below the sea surface from a 50m research vessel, the R/V Acoustic Explorer, measuring bioluminescence, seawater temperature, and salinity (Lapota and Losee 1984, Lapota et al. 1988, 1989). A vertically deployed bathyphotometer capable of measuring bioluminescence, temperature, salinity, beam attenuation, and chlorophyll fluorescence to a depth of 100m was used at 4 month intervals (summer, fall, winter, spring) at various stations in the Bight to examine the seasonal changes in the biological and physical structure of the water column (Lapota et at. 1989). Both systems were calibrated with the luminescent bacteria *Vibrio harveyii* in a Quantalum 2000 siliconphotodiode detector. The detector calibration is traceable to a luminol light standard (Matheson et al. 1984).

#### **2.2 Plankton and seawater analysis**

Water and plankton samples were collected at 10 stations within the Bight (Figure 1). Monthly transits were made from March 1994 through June 1996 from SCI to SDB to measure surface (3m depth) bioluminescence and collect plankton and seawater samples to determine Chl *a* content. At SDB, weekly plankton and water samples were taken for 4 years while monthly plankton and water samples were collected at SCI for 2.5 years. Because plankton abundance within SDB is usually high, 10 L water samples were concentrated while 40 l samples were filtered for plankton at SCI. Fifteen-liter water samples were collected and filtered from select bathyphotometer depths on the quarterly stations (10, 20, 30, 40, 50, 70, and 90 m). This was accomplished by discharging the bathyphotometer's effluent from its submersible pump through a 130-m long, 2.54 cm (I.D.) hose into a 15 liter Imhoff settling cone. The bottom of the cone was modified with a valve that allowed water to be filtered into collection cups fitted with 20-µm porosity netting. One liter of seawater (unfiltered) was also collected at the each of these depths and frozen in precleaned polycarbonate bottles for later chlorophyll and nutrient analysis. Plankton samples were preserved in a 5% formalin seawater solution. Bioluminescent dinoflagellates were identified to the species level when possible. Chlorophyll *a* was extracted from the seawater samples using standard methods (APHA 1981) and measured by fluorescence as an estimate of biomass on a Turner Model 112 fluorometer (Sequoia-Turner Corp., Mountain View, CA, U.S.A.) and reported as µg L-1.

Fig. 1. Bioluminescent study area and cruise track of stations within the Southern California Bight.

#### **2.3 Upwelling, rainfall, and seawater nutrient data bases**

Upwelling indices (North Pacific Ocean wind-driven transports) were collected from 1992 through 1996. The indices were computed for 33°N latitude (Schwing et al. 1996) and represent monthly average surface pressure data in cubic meters per second along each 100 m of coastline (Bakun 1973, Eppley 1986). Monthly rainfall data were acquired from the National Weather Service in San Diego. Nutrient and Chl *a* data were accessed from archived CALCOFI data (1992-1996) in the Bight and were averaged along CALCOFI lines 90 and 93 which run west from San Diego to the north and south of San Clemente Island (Hayward et al. 1996). Nitrates (µm L-1) and Chl *a* (µg L-1) along each of the CALCOFI transit lines (stations 93-26 to 93.45 and 90-28 to 90.53) were averaged from the surface to a depth of 50m for 12 cruises conducted from September 1992 through April 1995. These data were used to calculate correlations with bioluminescence, rainfall, and upwelling at SDB.
