Particulate organic carbon (POC) samples were collected in the Amazon River plume and adjacent ocean in May/June 2010 during high river discharge conditions and in September/October 2011 during low river discharge (onboard the R/V Knorr and R/V Melville, respectively, as part of the ANACONDAS expeditions; Medeiros et al., 2015).

Stations sampled during high discharge conditions are labeled H followed by the station number, while during low discharge they are labeled L followed by the station number.

Suspended samples were collected at the surface (~2 meters (m)), immediately below the plume (at ~20 m) and at depth (~1000 m and 2000 m) using CTD-rosette casts. At key oceanic stations, more highly resolved vertical profiles were also collected, including samples at the chlorophyll-a maximum and oxygen minimum depths. Seawater was filtered through 0.7-micrometer (µm) Whatman GF/F filters (pre-combusted at 450 degrees Celsius (°C) for 5 hours), carefully wrapped using pre-combusted aluminum foil, and kept frozen at -20°C until analysis. Samples were processed within 1-2 weeks after the end of the expeditions, minimizing the effects of any possible degradation that may have occurred during storage.

Prior to analyses, POC samples were allowed to dry at room temperature. Biomarkers were extracted from dried POC samples as in Medeiros et al. (2012) with a mixture of dichloromethane:methanol (2:1, v/v) using accelerated solvent extraction (ASE 350, Dionex) at 100°C and 1000 psi (3 static cycles). The extracts were concentrated in a RapidVap to about 2 milliliters (mL), then further concentrated to 500 microliters (μL) using a stream of ultra-high purity nitrogen gas. Aliquots of the total extracts were converted to their trimethylsilyl derivatives using N,O-bis-(trimethylsilyl)trifluoroacetamide (BSTFA) containing 1% trimethylchlorosilane (TMCS) and pyridine (Pierce) for 3 hours at 70°C. Aliquots of 1 μL of silylated total extracts were analyzed within 24 hours using an Agilent 6890 gas chromatograph interfaced with an Agilent 5975 mass selective detector (GC-MS). A DB5-MS capillary column (30 m x 0.25 mm I.D. and film thickness of 0.25 μm) was used with helium as the carrier gas. The injector and MS source temperatures were maintained at 280°C and 230°C, respectively. The column temperature program consisted of injection at 65°C and hold for 2 minutes, temperature increase of 6°C per minute to 300°C, followed by an isothermal hold at 300°C for 15 minutes. The MS was operated in electron impact (EI) mode with an ionization energy of 70 eV. The scan range was set from 50 to 650 Da and the samples were analyzed in splitless mode.

Data were acquired and processed with the Agilent-Chemstation software. Individual compounds were identified by comparison of mass spectra with literature and library data, comparison of mass spectra and GC retention times with those of authentic standards and/or interpretation of mass spectrometric fragmentation patterns. Compounds were quantified using the total ion current (TIC) peak area and converted to compound mass using calibration curves of standards.