README: Biological and physical controls on multidecadal acidification in a eutrophic estuary

https://doi.org/10.5061/dryad.6m905qg6h

Carbonate Saturation State and Net Ecosystem Metabolism datasets from Elkhorn Slough estuary, CA. Including code used to generate these datasets, spectral analysis of decadal pH datasets and nutrients, and Generalized Additive Mixed Models (GAMMs) of the long-term trends and drivers of pH in the estuary.

Description of the data and file structure

“Diel_water chemistry.csv”; Description: Water samples collected hourly for 24 hours each season at 6 sites in Elkhorn Slough, CA, using an ISCO autosampler and temperature and pH measured in situ with a HOBO pH logger; Headers: Site (Volunteer monitoring sites, “APC” Azevedo Central Pond, “AP” Azevedo Pond, “KP” Kirby Park, “BSE” Bennett Slough East, “JR” Jetty Road North, “SKL” Skipper’s Landing), Month (seasonal sampling in August, February, May, November), Hour (time of sample collection, Alkalinity_mgL (Alkalinity from sulfuric acid titration in mg/L units), Salinity_ppt (Salinity with YSI in ppt), Temp_C (Temperature from HOBO in Celsius), pH_Field (pH from HOBO in NBS units), pH_Field_adj20oC (Field measures of pH adjusted to 20 degrees Celsius), pH_Lab (pH measured on lab samples with YSI), Arag_saturation (Aragonite saturation in Omega units modeled from the Alk, Sal, Temp, and pH data). Cells containing “n/a” values indicate missing data because of a lack of data collected for this parameter at that site and time point.

“Monthly_water chemistry.csv”; Description: Water samples collected monthly over a year November 2018 to October 2019 at 6 sites in Elkhorn Slough, CA; Headers: Date (Day of collection), Time (timing of sample collection), Site (Volunteer monitoring sites in Elkhorn Slough, CA, “APC” Azevedo Central Pond, “AP” Azevedo Pond, “KP” Kirby Park, “BSE” Bennett Slough East, “JR” Jetty Road North, “SKL” Skipper’s Landing), Alkalinity_mgL (Alkalinity from sulfuric acid titration in mg/L units), Salinity_ppt (Salinity with YSI in ppt), Temp_C (Temperature from a YSI in Celsius), pH_Field (pH from a YSI in NBS units), Arag_saturation (Aragonite saturation in Omega units modeled from the Alk, Sal, Temp, and pH data).

“Metabolism_NEM.csv”, Description: Metrics of ecosystem metabolism created using the water monitoring data from 4 sites in Elkhorn Slough, CA, using the SWMPr R package (Beck, 2016); Headers: Date (Values represent one day), Site (National Estuarine Research Reserve System-wide monitoring sites in Elkhorn Slough, CA, “AP” Azevedo Pond, “NM” North Marsh, “SM” South Marsh, “VM” Vierra Mouth), DOF_d (Mean flux of dissolved oxygen during the daytime in units mmol m-2 hr-1), D_d (Mean exchange of gas air-sea during the daytime in units mmol m-2 hr-1), DOF_n (Mean flux of dissolved oxygen during the nighttime in units mmol m-2 hr-1), D_n (Mean exchange of gas air-sea during the nighttime in units mmol m-2 hr-1), Pg (Gross production in units mmol m-2 d-1), Rt (Total respiration in units mmol m-2 d-1), NEM (Net ecosystem metabolism Pg + Rt in units mmol m-2 d-1). Cells containing “n/a” indicate missing data because of the lack of dissolved oxygen data available at this time point and site (missing dissolved oxygen data in the DOF_d, D_d, DOF_n, or D_n columns also results in “n/a” values indicating missing data for the calculated metabolism metrics Pg, Rt, and NEM).

Sharing/Access information

Data is described in the publication titled “Biological and physical controls on multidecadal acidification in a eutrophic estuary”.

Additional publicly available datasets used in the paper and R code including Water quality, Nutrients, and Meteorology monitoring data can be accessed from the National Estuarine Research Reserve Systemwide Monitoring Program (NOAA, 2021), at http://www.nerrsdata.org. Upwelling data is available from the NOAA Environmental Research Division (Jacox et al., 2018), at https://oceanview.pfeg.noaa.gov/products/upwelling/intro

Code/Software

“Models and Figures.R”; Software: Run using coding language R version 4.0.5.

Use: Generating the figures in the publication including Timeseries plots (Figure 2b and Figure S4), Spectral analysis with “spectrum” function in Base R, Calculating Omega Aragonite, Calculating Net Ecosystem Metabolism, Graphs of Seasonal patterns of nitrate, metabolism (Figure 3a,b), Seasonal and diel patterns of aragonite saturation, alkalinity, and salinity (Figure 3c,d and Figure S5), Modeling pH using GAMMs over time and comparing drivers of pH (Figure 4, Table 1 and Table S8).

Input data: Original data generated in the study: “Diel_water chemistry.csv”, “Monthly_water chemistry.csv”, “Metabolism_NEM.csv”. Publicly available data: Water quality, nutrients, and meteorology monitoring data from the National Estuarine Research Reserve Systemwide Monitoring Program (NOAA, 2021), at http://www.nerrsdata.org; Upwelling data is available from the NOAA Environmental Research Division (Jacox et al., 2018), at https://oceanview.pfeg.noaa.gov/products/upwelling/intro

Packages: “janitor” (Firke S, 2023); “ggplot2” (Wickham H, 2016); “dplyr” (Wickham H, François R, Henry L, Müller K, Vaughan D, 2023); “lubridate” Garrett Grolemund, Hadley Wickham, 2011); “SWMPr” (Beck, 2016); “seacarb” (Jean-Pierre et al., 2021); “mgcv” R package (Wood, 2011)