DOI: 10.5061/dryad.6m905qg6h
title: Biological and physical controls on multidecadal acidification in a eutrophic estuary

description: Estuaries support many ecologically and economically important resources
 that are especially vulnerable to ocean acidification from rising
 anthropogenic CO2. However, complex local processes in estuaries
 complicate and may disguise long-term pH trends. For example, terrestrial
 nutrient runoff and marine coastal upwelling may exacerbate pH variability
 and declines. We investigated eutrophication impacts on acidification in a
 central California estuary, Elkhorn Slough, which receives high nutrient
 loads from intensive surrounding agriculture and upwelling of the
 California Current System. We examined drivers of acidification including
 nutrients, ecosystem metabolism, and upwelling by modelling pH trends over
 20 years using a Generalized Additive Mixed Model at four sites from the
 National Estuarine Research Reserve Systemwide Monitoring Program and
 collected additional water samples to calculate aragonite saturation. Our
 models revealed acidification trends over two decades which were more
 pronounced near the marine inlet. Near the marine inlet, high nutrient
 levels and lower buffering are associated with the greatest rate of
 acidification in the estuary, which was four times greater than the trend
 from anthropogenic CO2 alone. However, tidally restricted areas
 experienced a different acidification pattern. A tidally restricted site
 recorded higher mean pH and aragonite saturation and increased pH levels
 associated with stronger upwelling conditions supplying marine-sourced
 nutrients. Therefore, variable ecosystem metabolism and tidal cycles are
 threats to acidity in this location. The effects of enhanced seasonal
 cycles or long-term trends in different zones of the estuary have
 implications for monitoring with a temporal frequency and scale to capture
 coastal acidification risks in estuaries.
description: # Biological and physical controls on multidecadal acidification in a
 eutrophic estuary 
 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 .
 Upwelling data is available from the NOAA Environmental Research Division
 (Jacox et al., 2018), at
 ##
 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
 ; Upwelling data is available from the
 NOAA Environmental Research Division (Jacox et al., 2018), at
 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)