The water column in Monterey Bay (coastal California, USA) was sampled near-monthly from May 2014-February 2016 at stations M1 (36.747 \u00baN, 122.022 \u00baW) and M2 (36.697 \u00baN, 122.378 \u00baW), on board the RV Western Flyer or RV Rachel Carson using a CTD Rosette sampler (Sea-Bird Scientific, Bellevue, WA). For each hydrocast, the CTD collected data on conductivity, temperature, depth, dissolved oxygen (DO), total CO2, and transmissivity (turbidity). Additional samples were collected from 11-12 depths from the cast (0, 5, 10, 20, 30, 40, 60, 80, 100, 150, 200 m; 500 m included for 2015-2016) to measure nutrients (ammonia, nitrite, nitrate, silicate, phosphate), chlorophyll a and phaeopigment concentrations. These were processed using established methods as part of the Monterey Bay Time Series (http://www3.mbari.org/bog/Projects/CentralCal/summary/ts_methods_and_materials.htm; Pennington and Chavez 2000). Light penetration depth (LPD; 0.1-50 % of surface light) was estimated by secchi disk.
\nApproximately 1 L sample seawater was filtered using a peristaltic pump onto duplicate filters \u2013 10 \u00b5m polycarbonate (PCTE, Sterlitech; pre-filter), 0.2 \u00b5m GVWP (Millipore; final filter) \u2013 for molecular analysis from 6-10 depths per site per month (0-500 m depth). Samples were immediately frozen on liquid N2 and stored at -80\u00b0C upon return to laboratory until processing.
\nDNA was co-extracted with RNA using previously described methods (Smith et al. 2014a), with slight modification \u2013 both 0.1 and 0.5 mm sterile glass beads (BioSpec) were used for bead beating on the FastPrep (Thermo) and fresh -mercaptoethanol was added to Lysis/Binding buffer (10 \u00b5L per mL) immediately before extraction. Concentration of DNA was measured using a Qubit fluorometer (Invitrogen). Gene abundance was determined using published methods for total archaeal amoA (Francis et al. 2005), water column group A (WCA) and water column group B (WCB) amoA (Beman et al. 2008); modified to TaqMan assay, (Mosier and Francis 2011), and two archaeal nirK groups (AnirKa and AnirKb; Lund et al. 2012).\u00a0
\nWater samples were collected from 6-10 depths for nitrification rate measurements using 15NH4Cl as a tracer. Sample seawater was spiked with 15NH4Cl, and placed in ship-board seawater flow-through incubators for 24 h. Incubations were carried out in the dark or at estimated in situ light using stainless steel tubes with pre-drilled evenly spaced and sized holes (Pennington and Chavez 2000; Smith et al. 2014). At the end of incubations, samples were filtered (0.2 \u00b5m) and frozen at -20 \u00baC. \u03b415N values were measured from NOx in each sample, converted to N2O via the bacterial denitrification assay (Sigman et al. 2001) using a ThermoFinnigan Gas Bench and PreCon trace gas concentration system interfaced with the Delta VPLUS isotope-ratio mass spectrometer (Bremen, Germany) at the UC Davis Stable Isotope Facility.
Samples collected from the Monterey Bay Time Series from May 2014 to February 2016. These data include CTD, nutrient, chlorophyll a and paeopigment concentration data.\u00a0
\nThese data were published in Tolar et al., submitted (Table S1)
BCO-DMO processing notes:
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