Dataset: Depth profiles of nutrients and dark carbon fixation rates collected from the San Pedro Ocean Time-series (SPOT) R/V Yellowfin cruise in the San Pedro Basin on February 19, 2025

Water samples for nutrient analyses were collected from CTD Niskin bottles at discrete depths (15–100 m) from a single CTD cast. Approximately 40 mL of seawater was filtered onboard through 0.22 μm sterile syringe filters (Basix™ PES) and immediately frozen using an ethanol and dry ice bath prior to storage. Ammonia concentrations were determined using the o-phthaldialdehyde (OPA) fluorescence method following Holmes et al. (1999). Nitrite concentrations were measured spectrophotometrically using the sulfanilamide–NED method as described in Grasshoff et al. (1999). Nitrate concentrations were determined using the vanadium(III) chloride reduction method following García-Robledo et al. (2014).

For dark carbon fixation measurements, seawater was collected from CTD Niskin bottles from the same CTD cast and maintained in the dark at near in situ temperature. Four subsamples (90 mL each) were transferred into separate 110 mL acid-cleaned HDPE brown bottles. All subsamples were collected from the same Niskin bottle at each depth and divided into replicate incubations. All bottles were amended with approximately 6 μCi of 14C-labeled bicarbonate. One subsample was treated with 2.5% glutaraldehyde as a killed control, while the remaining three subsamples were incubated as biological replicates. Incubations were conducted in the dark at temperatures approximating in situ conditions (~15 °C for the 15m sample and ~11 °C for deeper samples). After ~60 hours of incubation, samples were processed following standard 14C carbon fixation protocols, including filtration and radioactivity measurement by liquid scintillation counting.