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- SUPPLEMENTARY INFORMATION -
Enhanced Transfer of Terrestrially-Derived Carbon to the Atmosphere in a Flooding
Event
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Thomas S. Bianchi, Fenix Garcia-Tigreros, Shari Yvon-Lewis, Michael Shields, Heath J.
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Mills, David Butman, Christopher Osburn, Peter Raymond, Christopher Shank, Steven F.
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DiMarco, Nan Walker, Brandi Reese, Ruth Mullins, Antonietta Quigg, George R. Aiken,
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and Ethan L. Grossman
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Background
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The chemical and biological signals we observed in this flooding event are not only
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reflective of large-scale events, analogous to long-term changes in precipitation in the upper
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basin from global climate change, but also processes that are normally more cryptic in the overall
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biogeochemistry of these river-dominated systems. Moreover, flooding events are likely to
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continue to occur if the precipitation changes we are observing in North America are a reflection
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of what to expect in future years. Our previously observed surface water pCO2 values from
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April 2011 in this region ranged from 100 ppm (a net sink) on the shelf to 2000 ppm in the
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freshwaters of the Atchafalaya near Morgan City, LA (a net source to the atmosphere).
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Having this pre-flood data along with other DOC, dissolved lignin, and microbial
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community structure that we have been measuring at our stations in this region for the past two
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years provides an ideal foundation to determine how much of this terrestrially-derived organic
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matter is being consumed pre-and post-flood. An event of this magnitude can extend previously
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reported gradients of CO2 source waters (heterotrophic respiration dominated including lignin
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degrading populations) beyond previously described CO2 sink areas (primary production
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dominated). A biological understanding of these microbial population shifts is critical to predict
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the environmental impact of future events and potentially provide mitigation strategies.
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Watershed studies indicate the collapse of variance of concentration of variables like DOC when
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moving up in watershed size.
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pCO2 and fluxes
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The metabolic state of an ecosystem can be described by the balance between gross
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primary production (GPP) and total respiration (R). In a heterotrophic system, there is more CO2
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being produced from the breakdown of allochthonous organic matter than inorganic carbon being
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consumed through photosynthesis by phytoplankton and macrophytes (R > GPP) [Raymond and
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Bauer, 2000]. Large rivers tend to be heterotrophic systems where inorganic carbon is outgassed
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as CO2, stored during sediment burial or exported to the coastal ocean as dissolved inorganic
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carbon (DIC) [Aufdenkampe et al., 2011]. High concentrations of CO2 in rivers can be a result of
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(1) soil respiration and mineral weathering imported into rivers, (2) in situ respiration of organic
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matter, (3) respiration of macrophytes, or (4) through photochemistry of riverine organic matter.
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Contrary to large rivers, river plumes and the coastal ocean are typically autotrophic systems
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[Guo et al., 2012; Borges et al., 2005].
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Results
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Oxygen isotopes
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Depending on the time of year, Atchafalaya River water can be the dominant source of
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freshwater on the Louisiana shelf, eclipsing the Mississippi River [Bianchi et al., 2010, and
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references therein] To determine if there were differences in the relative sources of freshwater
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from these two rivers during the 2011 flood, the 18O-salinity relationship was used as a water
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source tracer. June 2011 waters show the expected strong relationship between 18O and
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salinity, with a y-intercept of Atchafalaya Bay estuary (“Atch”) and C-transect waters of -5.68
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±0.08‰, identical to the 18O of Atchafalaya River samples (-5.76 ±0.03‰; R1-R5) (Figure A1).
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These values are typical for June/July Mississippi waters [-5.75 ±0.39‰; 2000-01: Lee and
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Veizer, 2003], and are slightly lower (more negative) than the average for Atchafalaya River
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waters for this period (-5.21±0.42‰). The Atchafalaya River includes water from the Red River,
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which is typically higher in 18O [mean 18O = -3.6‰; Coplen and Kendall, 2000]. Slight
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influence of Red River water may account for the slight 18O enrichment of water at stations R1-
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R5 and Atch relative to the 18O-S trend for offshore waters, which has an intercept of -6.06
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±0.10‰ (Figure A1). Overall, the close 18O-S relationship between offshore waters and R1-R5
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and Atch waters points to the dominance of Mississippi-derived waters in the Atchafalaya River
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and its estuary.
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pCO2
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Time series of the measured dissolved pCO2 and calculated fluxes for the three sampling
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cruises (pre-flood, during flood and post-flood; that is, April, June and August respectively) all
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show elevated pCO2 concentrations in the river, while the June and August cruise data show
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supersaturation extending beyond the river into the bays (Figure A2, main text Figure 1).
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Dissolved pCO2 concentrations in the Atchafalaya River reached levels twice as high during the
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flood cruise than during the pre- and post-flood cruises (4382 ppm vs 1876 ppm and 2131 ppm
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respectively). This increase in dissolved pCO2 is most likely due to the increased in labile
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terrestrial carbon and its oxidation to CO2 by heterotrophic populations in the river. The largest
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CO2 flux to the atmosphere for each cruise occurred in the Atchafalaya River where CO2 flux
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reached 2103 mmol m-2 d-1 for April, 639 mmol m-2 d-1 for June and 1118 mmol m-2 d-1 for
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August. Unlike the dissolved pCO2 values, the highest effluxes occurred in April and August.
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This was due to low wind speeds during the cruise in June (Figure A3). The air-sea fluxes are
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function of the air-sea concentration gradient and the gas transfer velocity which has a quadratic
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relationship to wind speed (see calculations for air-sea fluxes below).
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Air-sea fluxes
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Air-sea fluxes of CO2 were calculated using the following equation:
𝐹𝐶𝑂2 = 𝑘𝑠 ∙ ∆𝑝𝐶𝑂2
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where 𝐹𝐶𝑂2 is the air–sea flux (mmol m-2 d-1) with negative fluxes indicating CO2 uptake by the
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ocean; k (m d-1) is the gas transfer velocity; s is the solubility of CO2 in seawater calculated from
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sea surface temperature and salinity [Weiss,1974]; and, ∆𝑝𝐶𝑂2 is the difference between the
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partial pressure of CO2 in surface water (pCO2sw) and the partial pressure of CO2 in the
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atmosphere (pCO2atm).
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Determining the gas transfer velocity (k) for shallow estuaries and rivers is more complex
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than in the open ocean and is influenced not only by wind speed but by tidal currents and bottom
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stress. Consequently, in this paper the gas transfer velocity was calculated using the Jiang et al.
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(2008) parameterization for rivers and marine-dominated rivers:
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2
𝑘600 = 0.314 ∙ 𝑈10
− 0.436 ∙ 𝑈10 + 3.990
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where k600 is the gas transfer velocity at the Schmidt number of 600 and U10 is the wind speed
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normalized to 10 m above the water surface. This parameterization was produced by regressing
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literature data in coastal environments and compiling the most recent measurements. Wind
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speeds for April and August were directly measured on board. Wind speeds for June 2011 were
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obtained from a CIS buoy
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Area Calculations
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The areas in Figure A4 were created and calculated in ESRI ArcGIS 10.1. The map
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projection was designed as a Lambert Azimuthal Equal Area with center latitude of 29.5ºN and
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center longitude of -90.53ºE and chosen to coincide with MODIS true color (R,G,B enhanced)
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satellite imagery provided from the Earth Scan Lab at Louisiana State University
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(www.esl.lsu.edu) detailing the extent of floodwaters into the Atchafalaya Bay (main text Fig. 1).
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Base layers, noted in parentheses in the figure, were downloaded and from the National Oceanic
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and Atmospheric Administration (high resolution coastline), US Geological Survey (rivers),
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Louisiana State wide GIS Atlas (state bounds, cities), and Texas Natural Resources Information
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System (coastal bathymetry) websites and re-projected into the map projection. Regional extents
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were established by first creating shape-files along the coastline with edge boundaries
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determined by the pCO2 changes during the April 2011 flood. Regions were generalized to
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major boundaries of the Atchafalaya Bay and Mississippi River and did not include small
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tributaries, channels. Small islands, marsh, wetlands, or other low-lying areas were not excluded
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from the region shape-files. Regions were also constrained to the longitude extents, -91.0º E and
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-92.5º E of the data collected during April 2011 cruise. Six regions were created starting inshore
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and moving offshore: River, Inner Bay, Middle Bay, Outer Bay, Inner Coastal Shelf, and Outer
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Coastal Shelf. Areas for each region shapefile were calculated in ArcGIS (Figure A4 and main
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text Table 1).
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Using these areas and the mean CO2 flux to the atmosphere for each region, we
calculated the mass flux of carbon to the atmosphere for April, June and August (Pre-flood,
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during flood, post-flood). The regional net carbon fluxes to the atmosphere not including the
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river (dark brown) are -2.66, 4.36 and -0.22 Gg-C d-1 for April, June and August. The net fluxes
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including the river are -2.16, 4.71 and -0.009 Gg-C d-1 for April, June and August. Compared to
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previous measurements of CO2 concentration in the lower Mississippi River (New Orleans
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Carrolton water treatment), there was a distinct peak in during the flood, but other peaks like this
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have existed prior to this flooding event as well as well (Figure A5).
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DIC and Total Alkalinity
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In addition to the loss of inorganic carbon to the atmosphere, the mass flux of inorganic
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carbon from the river is a source to the bays, while the mass flux to the shelf is a sink. Using the
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observed dissolved inorganic carbon (DIC) concentrations along with dissolve pCO2
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concentrations, the air-water fluxes and some primary production rates (Tables A1 and A2), we
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can estimate the amount of respiration that could have occurred in the bays in April and June
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(Figure A6). The estimated respiration in the Bays is:
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Respiration = Primary Production in Bays + Net Flux CO2 to Atmosphere from Bays + Mass
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Flux of DIC out of Bays + Mass Flux of CO2 out of Bays – Mass Flux of DIC from River to Bays
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– Mass Flux of dissolved CO2 from River to Bays
(1)
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April: During the April cruise the DIC concentrations were fairly uniform along the mixing line
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from the river to the shelf (Figure A7). The flow rate for the lower Atchafalaya was 5578 m3 s-1.
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The mass fluxes of DIC and CO2 from the Atchafalaya River into the Bays were 9.77 x 108 mol-
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C d-1 and 2.96 x 107 mol-C d-1, while the mass fluxes out of the Bays were 9.44 x 108 mol-C d-1
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and 3.38 x 106 mol-C d-1 for DIC and dissolved CO2. The net flux of CO2 to the atmosphere
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from the Bays was -1.48 x 108 mol-C d-1, and the measured primary production rate was 8.63 x
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107 mol-C d-1. The estimated respiration rate is negative at -1.21 x 108 mol-C d-1, suggesting that
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there was an additional carbon sink present.
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June: During the June cruise the DIC concentrations were elevated in the Atchafalaya
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River and fairly uniform along the mixing line from the Bays to the shelf (Figure A7). The flow
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rate for the lower Atchafalaya was 6548 m3 s-1. The mass fluxes of DIC and CO2 from the
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Atchafalaya River into the Bays were 1.26 x 109 mol-C d-1 and 6.9 x 107 mol-C d-1, while the
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mass fluxes out of the Bays were 1.15 x 109 mol-C d-1 and 2.18 x 107 mol-C d-1 for DIC and
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dissolved CO2. The net flux of CO2 to the atmosphere from the Bays was 4.44 x 108 mol-C d-1
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(Table A2). For this cruise, there were no measurements of primary production. The chlorophyll
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concentration observed in the Bays in June was 9.024 μg L-1 which was 40% higher than the
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chlorophyll concentration in the river. Some primary production was needed to increase this
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chlorophyll concentration. If we assume a rate equal to that observed in April, the estimated
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respiration rate is 3.70 x 108 mol-C d-1, suggesting that up to 83% of the CO2 flux to the
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atmosphere could be sustained by in situ respiration. If we also assume that the additional
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carbon sink estimated for April was also present in June, the estimated respiration rate needed to
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sustain the carbon concentration in the Bays was 3.70 x 108 mol-C d-1, suggesting that
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approximately 56% of the flux of carbon to the atmosphere could be sustained by respiration. .
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Finally, the combination of PCA results and spectral data from June (Table A3) suggests that
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CO2 efflux was higher when there was more TDOC material in the surface waters – the role of
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terrestrially-derived POC was not investigated.
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Methods
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Oxygen isotopes
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Samples for oxygen isotopic analyses of water were collected in Nalgene bottles with
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screw caps wrapped with electrical tape. Oxygen isotopic compositions of waters were
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determined on 2 ml water samples by cavity ring-down spectroscopy (Picarro model L2120-i).
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Six 0.95-l injections were performed using a 5-l syringe. The first three measurements were
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discarded as a precaution against memory effects and the last three injections were evaluated for
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memory effects. Only injection of one sample showed evidence for memory effects and was
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discarded. Data are calibrated with the J-GULF working standard (+1.14‰ relative to
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VSMOW). Forty percent of the samples were duplicated with an average difference between
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duplicates, a measure of precision, of 0.10‰.
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DOC and Dissolved Lignin
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Approximately 2 L of seawater was filtered through 47 mm (in diameter) 0.7 μm
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(nominal pore size) pre-combusted (450 ºC, 4h) Whatman glass-fiber filters (GF/F) with gravity
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filtration system (connected to the Niskin bottle with 2N HCl pre-washed silica tubing) on the
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ship to collect duplicate DOC samples [Guo et al., 1994]. DOC samples were filtered and stored
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frozen at -20 ºC in pre-combusted (450 ºC, 4h) 40-ml amber vials, which were sealed with 2N
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HCl washed Teflon-topped septa and plastic screw tops. Acidified filtered water samples (100
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μL of 2 N HCl added to remove inorganic carbon) were then analyzed for DOC on a Shimadzu
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TOC-VCSH/CSN, using high-temperature catalytic oxidation [Guo et al., 1994]. The detection
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limit on this instrument is 3.2 μM, with a precision within 2%, based on the coefficient of
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variation.
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Approximately 20 L of filtered water was collected by pumping water through a 0.2 m
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Nuclepore filter cartridge (Whatman Co.) for dissolved lignin collection. Solid phase extraction
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(SPE) was then used to collect DOM and lignin, according to the method of Louchouarn et al.
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[2000]. This was performed on pre-packed columns that contained 10 g sorption material
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composed of octadecyl carbon moieties (C18), that were chemically bonded to silica as support
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(C18-SPE Mega-Bond Elut; Varian).
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Freeze-dried SPE dissolved lignin samples were analyzed for lignin-phenols using the
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cupric oxide method of Hedges and Ertel [1982], as modified by Goni and Hedges [1992].
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Lyophilized DOM samples were weighed to include 3 to 5 mg of organic carbon and transferred
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to stainless steel reaction vessels containing CuO according to the method described by Bianchi
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et al. [2007]. Lignin oxidation products were analyzed with an Agilent 5890 Gas
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Chromatograph/5973 Mass Spectrometric Detector (GC-MS). Quantification was based upon
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the internal standard ARS and ethyl vanillin was added before extraction to account for
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extraction efficiency. New response factors were generated with each batch by using a mixed
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standard of the target compounds. The average standard deviations, based upon two replicates (n
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= 2), for the sum of lignin phenols is less than 9% while that for individual compounds ranged
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from 2 to 17%. Eleven lignin phenols, p-hydroxybenzaldehyde, p-hydroxyacetophenol, p-
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hydroxycoumaric acid, vanillin, acetovanillone, p-hydroxybenzoic acid, syringealdehyde,
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vanillic acid, acetosyringone, syringic acid and ferulic acid, were quantified and used as
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molecular indicators for source and diagenetic state of vascular plant tissue. Lamda-6 (Λ6) is
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defined as the sum of vanillyl (vanillin, acetovanillone, vanillic acid) and syringyl
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(syringaldehyde, acetosyringone, syringic acid) phenols, and Lamda-8 (Λ8) includes the
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cinnamyl (p-coumaric and ferulic acid) phenols. Total cinnamyl/vanillyl and
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syringyl/vanillylphenols represent C/V and S/V ratios, respectively. Ratios of vanillic acid to
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vanillin (Ad/Al)v, syringic acid to syringaldehyde (Ad/Al)s [Hedges et al., 1988], p-
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hydroxyl/(vanillyl + syringyl phenols) [P/(V + S)] [Dittmar et al., 2001] and 3, 5-
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dihydroxybenzoic acid/V were used as indices of lignin decay.
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River DOC concentrations, specific ultraviolet absorption (SUVA254), and percent hydrophobic
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acids (HPOA)
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Water samples were collected across the annual hydrograph from the Mississippi River at
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Belle Chase, LA (lat/long) and Atchafalaya River at Morgan City, LA () as part of the U.S.
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Geological Survey National Stream Quality Accounting Network (NASQAN) sampling
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program. All water samples were filtered in the field through Gelman AquaPrep 600 capsule
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filters (0.45 µm) that were pre-rinsed with sample water. Dissolved organic carbon
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measurements were carried out on a heated persulfate oxidation OI Analytical Model 700 TOC
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analyzer [Aiken et al., 1992]. UV-visible absorbance measurements were undertaken on a
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Hewlett-Packard photo-diode array spectrophotometer (model 8453) between 200 and 800 nm
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using a 10 mm quartz cell. All samples were analysed at constant laboratory temperature and
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sample spectra were referenced to a blank spectrum of distilled water. All absorbance data
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presented in this manuscript are expressed as absorption coefficients, a(λ), in units of m-1 [Hu et
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al., 2002]. SUVA254 values were derived by dividing the UV absorbance (A) at λ = 254 nm by
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the DOC concentration (mgL-1) and is reported in the units of liter per milligram carbon per
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meter [Weishaar et al., 2003]. The hydrophobic organic acid fraction (HPOA) was obtained
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following established protocols (Aiken et al., 1992; Spencer et al., 2010). In brief, samples were
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acidified to pH 2 using HCl and passed through a column of XAD-8 resin. The HPOA fraction
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was retained on the XAD-8 resin and then back eluted with 0.1 M NaOH.
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Molecular Characterization of Microbial Populations and Statistics:
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Water samples were collected from the five river stations (R1-R5), the Bay station
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(ATCH-1) and two Gulf stations (8C and AB5) during the June cruise (Figure A8). The
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Atchafalaya Bay and Gulf 8C stations were sampled every six hours over a 24 h period. From
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these cruises, samples were processed from the midnight and noon time points. A total of 500 ml
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of water collected at each location and time point were filtered through a 0.2 µm pore
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polycarbonate filter and immediately frozen at -20oC during the length of the cruise. Filters were
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shipped to the Mills Laboratory on dry ice and then transferred to -80oC for storage. Total
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nucleic acids were extracted from half filters using the Mills Extraction Method described in
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detail in Mills et al. [2012]. Nucleic acid extracts were treated with Turbo DNA Free (Ambion,
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Inc.; Austin, TX) according to manufacturer’s instructions to remove residual DNA co-extracted
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with the RNA. Reverse transcription of targeted 16S rRNA gene transcripts used the 518R
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reverse primer [Nogales et al., 1999] following methods previously published in Reese et al.
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(2012) and Mills et al. (2012). The resulting cDNA was sequenced at the Research and Testing
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Laboratory (Lubbock, TX) following standard laboratory procedures and quality control as
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described in Mills et al. (2012). A total of 196,090 sequences passed quality control and were
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taxonomically classified (percent of total sequence length that aligned with a given database
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sequence) using the NCBI Basic Local Alignment Search Tool (BLASTn).NET algorithm
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(accessed November 2011) [Dowd et al., 2005]. Predictions of functional diversity were
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determined using lineages classified to the genus level to ensure the highest likelihood of
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physiological description using a 16S rRNA-based classification. Sequences were clustered into
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operational taxonomic units (OTU) using the Ribosome Database Project (RDP; Michigan State
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University; Lansing, MI) using a 95% sequence similarity cutoff. Additional sequence analysis
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was performed within the RDP R Statistical Computing Package including Sorensen distance
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matrix calculations. The Sorensen similarity index compares the similarity of data sets and is
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defined as the number of groups shared divided by the total number of groups (Figure A8). A
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dendrogram was constructed from the similarity index using the Phylip draw tree program
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[Felsenstein, 1989] with graphic interface (http://www.phylip.com). Resulting tree outfile was
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visualized and formatted using NJ Plot v2.2 (Perriere and Gouy, 1996) and TreeView v0.5.0
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(http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/)
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DOM Absorption and Fluorescence
Water samples were filtered through 0.2 μm polyethersulfone filters and stored in 125
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254
mL pre-cleaned polycarbonate bottles at 4°C for 5 days prior to analysis. Each sample was
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warmed to ambient temperature (20°C) and its absorption spectra from 200 to 800 nm were
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measured on a Varian 300 UV spectrophotometer in a 10 cm quartz cell. After subtraction of a
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Milli-Q water blank, absorbance values were converted to Napierian absorption coefficients,
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a(λ), using the following algorithm:
a ( ) 
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2.303
  A( ) raw  A( )blank 
L
(1)
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where A(λ) is the raw absorbance measured of the sample (raw) and the MilliQ blank (blank),
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and L is the pathlength of the absorption cell, in meters. DOM absorption spectra were used to
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compute SR, the ratio of log-linearized slopes calculated over specific wavelength ranges (275-
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295 nm: 350-400 nm) [Helms et al., 2008].
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DOM fluorescence on 0.2 μm filtrates was measured on a Varian Eclipse
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spectrofluorometer. at 800 V for river samples and 950 V for ocean samples, each voltage setting
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calibrated internally to the water Raman signal and then to quinine sulfate equivalents (1 QSE =
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1 µg L-1 quinine sulfate in 0.1 N H2SO4; Stedmon and Bro, 2008). Milli-Q water was used as a
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blank and each fluorescence measurement was corrected for inner-filtering effects, lamp
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intensity (excitation mode), and detector response (emission mode).
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DOM excitation-emission matrices (EEMs) were concatenated from emission (Em) spectra
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sampled at every 2 nm from 300 to 600 nm and measured at excitation (Ex) wavelengths that
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were increased from 240 to 450 nm in 5 nm intervals.
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DIC and TAlk
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Dissolved inorganic carbon was determine coulometrically following the methods described in
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SOP 2 [Dickson et al., 2007]. Total Alkalinity was determined by Gran titration [Gran, 1952]
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following the methods described in SOP 3b [Dickson et al., 2007].
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pCO2
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Continuous underway measurements of surface water pCO2 (pCO2sw) and atmospheric
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pCO2 (pCO2atm) were made using a pCO2 system similar to that described by Pierrot et al.
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[2009]. Seawater was drawn from an intake at 3 m under the water surface and distributed
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through a manifold to different sensors and to an equilibrator. Surface seawater flowed
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continuously through the equilibrator while the headspace was recirculated. The equilibrator
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consisted of a small (~1 L) equilibrator in which seawater is sprayed through a nozzle at 3-4 L
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min-1. The spray maximizes equilibration of CO2 in the seawater with the headspace. The
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headspace inside the equilibrator was maintained at ambient pressure by a vent. The headspace
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from the equilibrator is circulated through a condenser and a Nafion dryer to extract all water
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vapor. For 15 minutes out of every 2 hours, the flow through detector switched to ambient air.
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Air was continuously pumped at 0.5-2 L min-1 through a 0.63-cm ID SynFlex tubing which was
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mounted on the mast at the bow of the ship to minimize contamination. The system was
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calibrated periodically with reference standards obtained from NOAA/AOML and Scott
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Specialty blended gases with concentrations of 0, 344, 441, 1500, 2250 and 4500 ppm. Three
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standards were run for 10 minutes per standard, and concentrations chosen were adjusted based
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on surface water pCO2. The analyzer used to measure the mole fraction of CO2 in the sample gas
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was a non-dispersive infrared analyzer built by LiCOR (Li-820). The main difference between
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the Pierrot et al. [2009] pCO2 system and the system used for this study is that Pierrot et al.
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[2009] used a second equilibrator on the vent intake.
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PCA Statistics
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Principle Components analysis (PCA) was conducted in Matlab (v 7.4) using singular value
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decomposition. Data for each variable were autoscaled to a mean of zero and a standard
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deviation of one.
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References
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Aiken G., D. M. McKnight, K.A. Thorn, and H. Thurman (1992), Isolation of hydrophilic
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573.
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Aufdenkampe, A., J.I. Hedges, and J.E. Richey (2001), Sorptive fractionation of dissolved
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Bianchi, T.S., L.A. Wysocki, M. Stewart, T.R. Filley, and B.A. McKee (2007), Temporal
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Coplen T.B., and C. Kendall (2000), Stable hydrogen and oxygen isotope ratios for selected sites
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nitrogen in the eastern Arctic Ocean as evident from D- and L-amino acids. Geochim.
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Dickson, A.G., C.L. Sabine, and J.R. Christian (2007), Guide to best practices for ocean CO2
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Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST). BMC
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Guo, L., C.H. Coleman, and P.H. Santschi (1994), The distribution of colloidal and dissolved
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Goni, M.A. and J.I. Hedges (1992), Lignin dimers: Structures, distribution, and potential
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Hedges, J.I. and J.R. Ertel (1982), Characterization of lignin by gas capillary chromatography of
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337
Absorption spectral slopes and slope ratios as indicators of molecular weight, source, and
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photobleaching of chromophoric dissolved organic matter. Limnol. Oceanogr., 53, 955-
339
969.
340
Hu, C.M., F.E. Muller-Karger, and R.G. Zepp (2002), Absorbance, absorption coefficient, and
341
apparent quantum yield: a comment on common ambiguity in the use of these optical
342
concepts. Limnol. Oceanogr., 47,1261–1267.
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Huguet, A., L. Vacher, S. Relexans, S. Saubusse, J.M. Froidefond, and E. Parlanti (2009),
344
Properties of fluorescent dissolved organic matter in the Gironde Estuary. Org.
345
Geochem., 40, 706-719.
346
Jiang, Li‐Q., W.J. Cai, R. Wanninkhof, Y. Wang, and H. Luger (2008) Air‐sea CO2 fluxes on
347
the U.S. South Atlantic Bight: Spatial and seasonal variability. J. Geophys. Res., 113,
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C07019, doi:10.1029/2007JC004366.
349
Lee D.H., and J. Veizer (2003) Water and carbon cycles in the Mississippi River basin: potential
350
implications for the northern hemisphere residual terrestrial sink. Global. Biogeochem.
351
Cycles, doi:10.1029/2002GB001984.
352
Louchouaran, P., S. Opsahl, and R. Benner (2000) Isolation and quantification of dissolved
353
lignin from natural waters using solid-phase extraction (SPE) and GC/MS SIM. Anal.
354
Chem., 72, 2780-2787.
355
Mills, H.J., B.K. Reese, and C. St. Peter (2012), Characterization of microbial population shifts
356
during sample storage. Front. in Extrem. Microbiol.: Deep Subsurf. Microbiol., 3,49. doi:
357
10.3389/fmicb.2012.00049.
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358
359
360
361
362
363
Nogales, E., M. Whittaker, R.A. Milligan, and K.H. Downing (1999). High resolution structure
of the microtubule. Cell 96, 79-88.
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sequence banks. Biochimie, 78, 364–369.
Reese, B.K. H.J. Mills, S.E. Dowd, J.W. Morse, Linking molecular microbial ecology to
geochemistry in a coastal hypoxic zone. Geomicrobiol., In press.
364
Shank, G.C., and A. Evans (2011), Distribution and photoreactivity of chromophoric dissolved
365
organic matter in northern Gulf of Mexico shelf waters. Cont. Shelf Res., 31, 1128-1139.
366
367
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Stedmon, C., and R. Bro (2008), Characterizing dissolved organic matter fluorescence with
parallel factor analysis: a tutorial. Limnol. and Oceanogr: Methods. 6, 572-579.
Weishaar, J.L., G.R. Aiken, B.A. Bergamaschi, M.S. Fram, R. Fujij, and K. Mopper (2003),
369
Evaluation of specific ultraviolet absorbance as an indicator of the chemical composition
370
and reactivity of dissolved organic carbon. Environ. Sci.Technol., 37, 4702–4708.
371
372
Weiss, R.F. (1974), Carbon dioxide in water and seawater: The solubility of a non-ideal gas.
Mar. Chem., 2, 203-215.
373
17
SUPPLEMENTARY INFORMATION
374
FIGURES
375
376
377
Figure A1. Oxygen isotope composition versus salinity for Atchafalaya River and Estuary
waters and Louisiana shelf surface waters.
378
379
380
381
382
18
SUPPLEMENTARY INFORMATION
383
384
385
386
387
388
389
Figure A2. Time series of dissolved pCO2 and fluxes of CO2 for cruises during (a) April 2011 (b)
June 2011 and (c) August 2011. The red dashed line indicates equilibrium with the atmosphere.
The gray shading highlights sampling stations with its corresponding station name.
390
391
19
SUPPLEMENTARY INFORMATION
392
393
394
395
396
397
398
Figure A3. Time series for wind speed, salinity and temperature during (a) April 2011 (b) June
2011 and (c) August 2011.The yellow shading highlights sampling stations with its
corresponding station name.
399
20
SUPPLEMENTARY INFORMATION
400
401
402
403
404
405
406
Figure A4. The six colored regions were created in ESRI ArcGIS 10.1 to determine areal extent
(km2) for the determination of areal pCO2 fluxes in Table 1: River (47.286, dark brown), Inner
Bay (241.471, light brown), Middle-Bay (1638.024, off-white), Outer Bay (1412.664, green),
Inner Coastal Shelf (2289.410, light blue), and Outer Coastal Shelf (4136.202, dark blue). Map
designed and area calculated in a Lambert Azimuthal Equal Area with center latitude of 92.5
and center longitude of -90.53. The stations occupied during the June cruise are shown.
407
21
SUPPLEMENTARY INFORMATION
6000.0
5000.0
pCO2 (uatm)
4000.0
3000.0
Series1
2000.0
1000.0
0.0
04/28/07 11/14/07 06/01/08 12/18/08 07/06/09 01/22/10 08/10/10 02/26/11 09/14/11 04/01/12
408
409
410
411
Figure A5. CO2 calculated from daily pH and alkalinity titrations made at the New Orleans
Carrolton water treatment facility. CO2 was calculated using CO2SYS using freshwater
dissociation constants.
22
SUPPLEMENTARY INFORMATION
412
413
414
415
Figure A6. Schematic of the movement of inorganic carbon into and out of the Bays.
23
SUPPLEMENTARY INFORMATION
2300
416
A)
DIC-June
DIC-April
2250
2200
417
2150
DIC (mol/kg)
418
419
420
2100
2050
2000
421
1950
422
1900
423
1850
Atch
Atch
0
2
4
6
8 10 12 14 16 18 20 22 24 26 28 30 32 34 36
Salinity
424
425
B)
426
2500
2450
427
2400
428
430
431
432
2350
2300
TAlk (mol/kg)
429
Figure A7. A) DIC and B) Alk from the river, Atch and 8C
stations in April (●) and June (■).
2250
Atch
2200
2150
2100
Atch
2050
June
April
2000
433
1950
1900
0
2
4
6
8 10 12 14 16 18 20 22 24 26 28 30 32 34 36
24
Salinity
SUPPLEMENTARY INFORMATION
434
25
SUPPLEMENTARY INFORMATION
435
436
437
438
439
440
441
442
Figure A8. Structure and function of the metabolically active water column microbial populations. A neighbor-joining dendrogram
was constructed based on 16S rRNA gene transcript sequence similarity. End nodes represent sample specific populations from two
Gulf shelf sites (AB5 and 8C), and the Atchafalaya Bay and river. The 8C and Atchafalaya Bay sites were sampled every 6 hours over
a 24 hr period. Samples from 8C were also collected at the water surface (Top), at 10 m below surface (Mid) and near bottom
(Bottom). Functional groups were determined by comparing sequences to previously identified lineages. Cyanobacteria sequences
were only reported associated with the photosynthesis group although they are capable of nitrogen fixation due to the high number of
sequences detected.
443
444
Table A1. Station locations and physcial and chemical parameters analyzed in surface waters in April, June, and August 2011 in the
445
Atchafalaya and Louisiana coast.
26
SUPPLEMENTARY INFORMATION
446
a.
Station
Latitude
08A
AB5
AB5
AB5
AB5
AB5
Atch
Atch
08C
29º02.4505 N
29º04.608 N
29º05.297 N
29º05.303 N
29º05.301 N
29º05.431 N
29º15 N
29º15 N
29º00.511 N 29º00.511 N 29º00.482 N
Longitude
89º34.6571 W 89º44.862 W
89º56.058 W
89º56.045 W
89º56.408 W
89º56.431 W 91º36 W
91º36 W
91º59.491 W 91º59.491 W 91º59.489 W 91º59.500 W 90º33.202 W
Date
Time (GMT)
Temperature (°C)
Salinity
SPM (mg/L)
DOC (µM)
10 minute average
dissolved pCO2 (ppm)
10 minute average CO2
sea-to-air Flux
(mmol/m2/d)
08C
08C
08C
10b
10b
10b
10b
29º00.508 N
28º37.531 N
28º37.541 N
28º37.556 N
28º37.556 N
90º33.197 W 90º33.175 W 90º33.175 W
25-Apr-11
26-Apr-11
26-Apr-11
26-Apr-11
26-Apr-11
26-Apr-11
28-Apr-11
28-Apr-11
28-Apr-11
28-Apr-11
29-Apr-11
29-Apr-11
29-Apr-11
30-Apr-11
30-Apr-11
30-Apr-11
17:06
1:14
5:14
11:04
17:05
23:06
5:00
11:00
18:16
23:04
5:00
11:00
23:00
5:00
10:57
16:48
N/A
25.58
N/A
24.37
24.29
24
23.77
23.94
23.55
23.42
34.3
22.3228
21.0641
21.1968
21.3980
21.7194
20.7679
26.5902
22.4108
32.3007
32.4567
32.1944
31.3259
32.1971
34.0388
34.5007
N/A
39.47
N/A
31.28
N/A
8.85
8.27
133.33
85.71
6.55
6.27
35.49
28.08
3.49
26.21
28.20
3.02
156
126
161
184
128
183
186
189
106
102
121
120
84
96
78
67
N/A
212.2
87.1
93.6
99.1
81.4
248.5
248.5
259.6
307.3
282.9
281.4
257.0
230.0
286.4
308.0
N/A
-34.6
-51.7
-47.9
-26.0
-83.9
-36.5
-43.0
-4.6
-10.5
-13.1
-18.6
-14.7
-17.4
-12.8
-7.8
N/A
5.798
0.154
0.051
0.718
3.422
1.224
0.453
0.333
0.832
0.619
0.434
0.634
0.045
25.79
Max Fl Ex (nm)
Max Fl Em (nm)
Max Fl (QSU)
BIX
HIX
SR
%C1
%C2
%C3
%C4
Chlorophyll a(ug/L)
Primary productivity
3
(mg C/m /h)
Dissolved Lignin Σ8
(µg/L)
Dissolved Lignin Σ6
(µg/L)
Dissolved Lignin
(Ad/Al)v
Dissolved Lignin
(Ad/Al)s
still to run
N/A
2.353
N Fix(-Cyano)
N Ox
N Red
Cyanobacteria
Fe Red
C-Acetogen
Methylotroph
C-Photosynthetic
447
Soil/Lig
27
SUPPLEMENTARY INFORMATION
448
b.
Station
Latitude
R1
R2
R3
29º36.4737 N
29º33.4393 N
29º31.9926 N 29º29.3146 N 29º22.2795 N
Longitude
91º14.8489 W 91º13.9859 W 91º16.7542 W 91º16.2275 W 91º22.9952 W 91º37.0791 W 91º37.2537 W 91º36.9744 W 91º36.9575 W 91º54.5351 W 91º59.5318 W 91º59.5424 W 91º59.5248 W 91º59.5018 W 90º33.4417 W 89º34.7149 W 89º56.0169 W
Date
R5
Atch
Atch
29º16.8942 N 29º17.1917 N
Atch
Atch
07C
08C
29º16.6951 N
29º17.0338 N
29º07.3684 N
29º00.4712 N 29º00.4700 N
08C
08C
08C
29º00.4724 N
29º00.4712 N 28º37.3837 N
10B
08a
AB5
29º02.4523 N
29º04.7765 N
20-Jun-11
20-Jun-11
20-Jun-11
20-Jun-11
20-Jun-11
21-Jun-11
21-Jun-11
21-Jun-11
21-Jun-11
22-Jun-11
22-Jun-11
22-Jun-11
22-Jun-11
22-Jun-11
23-Jun-11
23-Jun-11
23-Jun-11
Time (GMT)
15:33
16:13
16:50
17:26
18:38
5:15
10:58
17:05
23:30
2:15
5:00
11:00
17:36
23:30
9:00
16:00
18:26
Temperature (°C)
29.63
28.88
29.48
29.32
29.62
29.60
28.36
29.46
29.77
30.19
29.71
29.20
27.46
29.61
29.44
29.97
30.26
0.1647
0.1644
0.1639
0.1634
0.1640
1.8567
13.2613
15.4351
10.8696
N/A
26.7398
27.5423
27.5025
27.8052
30.2858
18.5585
12.1795
43.00
69.00
37.00
53.00
32.00 *
256.00
114.00
72.00
130.00
104.00
N/A
17.00
16.50
1.50 *
14.50
8.00
N/A
466
405
442
380
400
422
368
334
373
286
231
173
191
217
200
247
270
N/A
N/A
N/A
N/A
4319.1
842.4
901.3
N/A
587
561.1
568.5
332.4
314.9
307.7
N/A
N/A
N/A
Salinity
SPM (mg/L)
DOC (µM)
10 minute average
dissolved pCO2 (ppm)
10 minute average CO2
sea-to-air Flux
(mmol/m2/d)
N/A
N/A
N/A
N/A
624.5
86.5
91
N/A
74.4
72.9
90.5
-3
-2.5
-7.9
N/A
N/A
N/A
Max Fl Ex (nm)
240
240
240
240
240
240
240
240
240
240
240
240
245
240
240
240
240
Max Fl Em (nm)
432
434
426
432
436
430
438
422
438
430
434
420
438
438
440
440
440
34.39
36.01
33.49
33.61
33.65
34.47
20.63
18.62
22.11
8.21
6.10
5.49
5.15
6.35
2.92
11.91
17.50
Max Fl (QSU)
BIX
0.584
0.569
0.521
0.608
0.596
0.572
0.625
0.636
0.726
0.770
0.809
0.833
0.804
0.740
0.769
0.669
0.727
HIX
11.943
10.084
11.397
11.904
11.773
9.979
7.529
6.717
7.365
4.978
3.303
4.028
5.082
3.856
3.789
6.941
8.371
SR
%C1
0.904
0.912
0.955
0.947
0.907
0.910
0.997
1.039
0.993
1.160
1.345
1.243
1.237
1.285
1.308
1.104
1.020
0.696
0.654
0.689
0.687
0.694
0.662
0.631
0.618
0.626
0.561
0.497
0.528
0.577
0.531
0.566
0.628
0.642
%C2
0.157
0.152
0.156
0.155
0.155
0.145
0.135
0.132
0.132
0.108
0.094
0.099
0.112
0.099
0.114
0.118
0.131
%C3
0.114
0.145
0.115
0.115
0.115
0.149
0.166
0.175
0.169
0.203
0.209
0.210
0.150
0.203
0.121
0.155
0.155
%C4
0.032
0.048
0.040
0.044
0.036
0.045
0.068
0.076
0.073
0.128
0.201
0.164
0.161
0.167
0.199
0.098
0.073
Chlorophyll a(ug/L)
Primary productivity
5.481
4.981
4.727
5.478
6.492
11.007
9.840
7.574
7.676
8.020
3.398
3.110
3.322
4.362
1.367
17.309
23.722
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
25.9
14.3
9.1
8.8
6.3
4.4
14.5
6.1
1.6
1.1
0.8
0.9
N/A
1.2
0.8
N/A
3.6
(mg C/m3/h)
Dissolved Lignin Σ8
(µg/L)
Dissolved Lignin Σ6
(µg/L)
Dissolved Lignin
(Ad/Al)v
Dissolved Lignin
(Ad/Al)s
12.0
7.4
8.4
8.8
6.3
4.4
6.7
4.0
1.6
1.0
0.8
0.9
N/A
1.2
0.5
N/A
3.5
1.34
0.77
0.90
1.25
0.81
1.47
1.34
1.18
1.00
1.10
1.15
1.22
N/A
1.77
1.75
N/A
1.14
0.93
0.56
0.44
0.65
0.33
0.43
0.93
0.73
0.38
0.53
0.50
0.44
N/A
0.34
0.68
N/A
0.67
N Fix(-Cyano)
5.91
6.37
5.49
5.35
5.35
2.86
2.24
1.31
2.33
N/A
0.35
0.28
0.51
0.72
N/A
N/A
0.44
N Ox
2.83
1.81
1.77
2.06
1.54
0.77
0.41
0.02
0.21
N/A
0.04
0.06
0.00
0.00
N/A
N/A
0.00
N Red
10.54
11.63
11.91
11.21
8.55
11.56
5.32
2.03
5.08
N/A
2.14
2.67
2.47
3.11
N/A
N/A
1.26
Cyanobacteria
27.95
31.33
33.84
38.56
50.38
40.90
36.33
61.25
46.98
N/A
44.79
48.12
56.30
54.69
N/A
N/A
89.85
Fe Red
4.09
2.90
3.41
2.89
1.82
0.91
1.18
0.62
1.51
N/A
1.02
0.90
0.69
0.81
N/A
N/A
0.15
C-Acetogen
1.66
1.73
1.96
1.59
1.68
1.62
0.86
0.32
0.27
N/A
0.00
0.00
0.00
0.02
N/A
N/A
0.07
Methylotroph
3.60
2.63
2.78
2.43
1.63
1.26
1.06
0.28
1.06
N/A
0.67
0.53
0.35
0.46
N/A
N/A
0.05
29.30
32.62
35.16
39.66
52.13
41.73
37.62
62.05
47.55
N/A
44.85
48.20
56.37
54.80
N/A
N/A
91.55
8.11
6.46
6.41
5.64
4.05
4.45
2.36
2.05
1.21
N/A
1.87
1.40
1.79
2.11
N/A
N/A
0.44
C-Photosynthetic
449
R4
Soil/Lig
450
451
452
453
454
28
SUPPLEMENTARY INFORMATION
455
c.
Station
Latitude
08a
AB5
AB5
AB5
AB5
29º02.4559 N
29º05.4008 N
29º05.3924 N
29º05.3514 N
29º05.3122 N 28º37.6322 N
Longitude
89º34.4404 W
Date
10b
10b
10b
10b
08C
08C
08C
08C
R1
R2
R3
R4
28º37.6248 N
28º37.5938 N
28º37.6114 N
28º37.6533 N
29º00.5125 N
29º00.4962 N
29º00.5118 N
29º00.5335 N
29º36.2893 N
29º32.6427 N
29º29.7579 N
29º26.7014 N 29º15.8175 N 29º15.8137 N
89º56.1707 W 89º56.1950 W 89º56.1253 W 89º56.1514 W 90º33.1778 W 90º33.1681 W 90º33.1762 W 90º33.2205 W
10b
90º33.2287 W
91º59.3487 W 91º59.3504W
Atch
Atch
Atch
Atch
29º15.7492 N
91º59.3485 W 91º59.3643 W 91º14.6994 W 91º15.1814 W 91º16.1476 W 91º18.6368 W 91º36.7117 W 91º36.7035 W
29º15.7529 N
91º36.6866 W 91º36.7093 W
16-Aug-11
16-Aug-11
17-Aug-11
17-Aug-11
17-Aug-11
18-Aug-11
18-Aug-11
18-Aug-11
18-Aug-11
18-Aug-11
19-Aug-11
19-Aug-11
19-Aug-11
20-Aug-11
20-Aug-11
20-Aug-11
20-Aug-11
20-Aug-11
20-Aug-11
21-Aug-11
21-Aug-11
12:18
22:18
4:55
10:34
16:30
0:28
4:58
11:31
17:28
22:57
10:28
16:50
22:32
4:59
18:01
18:34
19:06
19:40
23:33
5:01
10:39
16:31
31.69
30.92
30.61
30.88
31.49
31.44
31.41
31.74
32.69
31.29
31.2
N/A
26.2738
27.4667
26.7104
26.5875
29.8085
29.6708
29.2987
29.314
29.4026
33.7019
33.7312
33.6492
33.6158
0.2525
0.2535
0.2534
0.2541
24.4768
27.1727
27.4164
26.1579
10.20
11.00
6.00
11.50
14.50
9.00
3.25
N/A
12.25
4.00
4.25 *
6.00
6.50
1.75
82.00
92.00
80.00
50.00
21.00
34.00
26.00
24.00
257
265
303
262
271
226
238
220
185
218
184
173
161
165
298
244
343
290
263
250
234
255
N/A
355.5
422.2
426.3
397.4
403.2
402.0
391.6
386.0
377.4
456.5
469.7
476.1
465.7
2064.4
1986.2
2094.7
1965.3
350.4
462.2
513.5
420.6
N/A
-0.8
7.3
12.3
2.7
0.5
0.3
0.4
0.4
0.2
2.2
1.7
6.2
6.3
72.6
296.3
358.8
503.7
4.1
3.6
2.8
1.1
Chlorophyll a(ug/L)
Primary productivity
2.773
3.246
3.060
2.663
0.647
0.661
0.663
0.930
0.636
0.476
0.306
0.282
0.385
10.854
11.920
5.453
12.199
(mg C/m3/h)
Dissolved Lignin Σ8
(µg/L)
Dissolved Lignin Σ6
(µg/L)
Dissolved Lignin
(Ad/Al)v
Dissolved Lignin
(Ad/Al)s
0.829
1.331
1.621
5.924
0.455
0.223
0.912
1.194
0.398
0.102
0.294
0.982
4.191
1.140
0.578
Time (GMT)
Temperature (°C)
Salinity
SPM (mg/L)
DOC (µM)
10 minute average
dissolved pCO2 (ppm)
10 minute average CO2
sea-to-air Flux
(mmol/m2/d)
21-Aug-11
32.95
Max Fl Ex (nm)
Max Fl Em (nm)
Max Fl (QSU)
BIX
HIX
SR
%C1
%C2
%C3
%C4
N Fix(-Cyano)
0.59
0.30
1.07
0.80
0.47
0.55
0.342857143
0.142816338
N Ox
0.04
0.00
0.00
0.06
0.01
0.00
0.028571429
0.057126535
N Red
1.98
0.30
1.99
2.37
0.20
1.00
2.285714286
0.9711511
36.02
80.44
46.19
51.77
71.93
51.87
65.68571429
70.15138532
Fe Red
0.88
0.27
1.27
1.03
0.38
1.10
0.828571429
0.342759212
C-Acetogen
0.00
0.00
0.00
0.00
0.04
0.00
0
0.028563268
Methylotroph
0.15
0.00
0.55
0.17
0.13
0.39
0.285714286
0.228506141
36.94
81.31
46.63
52.53
72.42
52.28
67.05714286
72.97914881
0.26
0.14
1.10
0.56
0.12
0.61
3.371428571
5.769780063
Cyanobacteria
456
C-Photosynthetic
Soil/Lig
457
458
459
460
461
462
29
SUPPLEMENTARY INFORMATION
463
Table A3. Mean concentrations, fluxes and areas for the regions shown in Figure A5 for April, June and August 2011. Values in
464
parenthesis are standard deviations. Arrows up and down indicate all areas represented by the average value shown.
River
(Dark
Brown)
Inner Bay
(Lt Brown)
April
Area pCO2
Flux
2
(km ) (ppm) (mmol m-2
d-1)
47
1821.8
892.5
(33.5)
(706.1)
241
June
pCO2
(ppm)
Flux
(mmol m-2 d-1)
pCO2
(ppm)
4213.1
(81.1)
604.1
(16.7)
2045.8
(54.6)
3715.4
(175.7)
526.5
(28.3)
1042.4
(65.8)
71.7
(26.0)
864.1
(34.7)
74.9
(15.8)
Middle Bay
(Off-White)
1638
Outer Bay
(Green)
1412
Inner Shelf
(Lt Blue)
2289
283.5
(15.6)
-12.1
(6.0)
595.5
(29.9)
Outer Shelf
(Dark Blue)
4136
296.4
(14.8)
-13.7
(4.4)
302.2
(9.6)
243.5
(10.1)
-35.5
(14.3)
August
Flux
(mmol m-2 d1
)
371.5
(322.2)
448.6
(142.3)
-1.9
(0.4)
15.0
(4.7)
467.2
(18.4)
3.4
(1.8)
-4.8
(2.8)
384.4
(27.5)
-0.1
(3.0)
465
466
467
30
SUPPLEMENTARY INFORMATION
468
Table A2. Pearson’s correlation (r) results for DOM qualitative
indices used as proxies for terrestrial and marine DOM sources.
All correlations were significant.
10 minute average pCO2 (ppm)
r values
p
values
Max Fl (QSU)
0.78
0.022
BIX
-0.84
0.010
HIX
0.72
0.043
SR
-0.71
0.047
469
470
471
472
31