Static chamber fluxes of carbon dioxide and methane from coastal wetlands on Upper Cape Cod, Massachusetts and supporting environmental data, 2021

Six sampling locations were established across several villages of Falmouth, MA for static chamber sampling. Two sampling locations were established at a site with natural, unrestricted tidal exchange at Sage Lot Pond, two in an impounded marsh at Flat Pond, one site in West Falmouth behind a Quaker Meeting House, and one site in Woods Hole behind Woods Hole Park. Each sampling location was equipped with three replicate collars for static chamber measurements and one pair of air/soil temperature sensors. The two sites at Sage Lot Pond were part of a prior study established in 2020 and data collected in 2020 from those sites is available at https://www.sciencebase.gov/catalog/item/62557ae8d34e21f8276f4879.
To facilitate static chamber CH4 and CO2 flux measurements, round PVC collars (55 cm inner diameter, 24 cm height, 3 replicates per sampling location (n = 6)) were inserted into the sediment surrounding intact vegetation to a depth of at least 10 cm more than four weeks prior to initial sampling to allow the soil to equilibrate from disturbance. On each sample collection date, we used a modular system of clear, round acrylic chambers to enclose the vegetation and sediment surface for flux measurement. Chamber sections were 55 cm diameter and 0.91 meters (m) tall. Depending on the height of the vegetation at the sampling location we used either one, two, or three stacked chambers for a total chamber height of 0.91, 1.83 or 2.74 m and empty chamber volume of 0.22, 0.43 or 0.64 cubic meters (m3). The topmost chamber always had a transparent lid permanently affixed with silicone caulking and a vent tube to allow for pressure equilibration. Two battery-powered fans (10 cm in diameter) were attached to the inside of the chamber to homogenize air and temperature sensors (HOBO TidbiT v2, Onset Computer Corporation) were mounted to the inside of the top and bottom chambers to record chamber air temperature. All samples were collected during mid-day hours between 10:00-14:00 local standard time. Chamber air was considered equilibrated based on visual inspection of the stability of a linear concentration change in the gases of interest, this was typically less than 60 seconds.
Field data required to calculate fluxes (i.e., chamber head space, chamber deployment time) were recorded on field datasheets and later entered into electronic spreadsheets. Concentrations of CH4 and CO2 during 2-5 minutes incubations were measured and recorded using a portable optical feedback-cavity enhanced absorption spectrometer (LI-7810 CH4/CO2/H2O Trace Gas Analyzer, LI-COR, Inc.) sampling at 1 Hz. Chamber flux incubations were conducted both in the light with transparent chambers to quantify net ecosystem exchange, and in the dark with opaque covering of the chambers to quantify ecosystem respiration in the absence of photosynthesis.
We used a sliding regression (“rollRegres” package in R, Christoffersen, 2019) to identify the 120-second window during the incubation where a simple linear regression of CH4 or CO2 concentration by time had a maximum R2. We verified that all linear models used to calculate flux had a significant slope (p less than 0.001) and an RMSE ≤ 1 ppm for CO2 and ≤ 10 ppb for CH4. Four CO2 measurements did not have a slope significantly different than 0, and therefore those fluxes were set to 0. Three additional CO2 measurements were rejected for low R2 and RMSE > 1 ppm.
We also assessed each incubation for non-linear changes in CH4 concentration over time as a signal of potential ebullition. When potential ebullition was observed, in addition to applying the sliding regression described above, we estimated CH4 concentration change based on the initial and final concentration of CH4 gas (VCS, 2015).
The rate of concentration change of CO2 and CH4 (slope or the difference between final and initial when ebullition was suspected) was converted to an area-based flux using the Ideal Gas Law and the volume and footprint of the chamber, along with measured chamber air temperature (pooled across the two temperature sensors). Calculations were executed with the “conc_to_flux” function in the R package “ecoflux” (Shannon, 2018).
This process step and all subsequent process steps (unless otherwise noted) were performed by the same person, Rebecca Sanders-Demott.
Christoffersen, B., 2019, rollRegres: Fast Rolling and Expanding Window Linear Regression. R package version 0.1.3. https://CRAN.R-project.org/package=rollRegres
Shannon, J., 2018, ecoFlux: Functions for ecological flux studies including sap flux and soil/stem C efflux (0.3.1). https://rdrr.io/github/jpshanno/ecoflux/
Verified Carbon Standard (VCS), 2015, Approved VCS Methodology VM 0033: Methodology for Tidal Wetland and Seagrass Restoration. Version 1.0, 20 November 2015, Sectoral Scope 14. Developed by Verra with Restore America’s Estuaries and Silvestrum. 1–115. https://verra.org/wp-content/uploads/2018/03/VM0033-Tidal-Wetland-and-Seagrass-Restoration-v1.0.pdf

Soil volumetric water content (VWC) integrated over the top 5 cm was measured (Meter Group Inc., TEROS-10) just outside each collar after gas sampling. Values were recorded by hand on a field data sheet and later entered into an electronic spreadsheet.

Photosynthetically active radiation (PAR) was measured concurrent with chamber sampling with a PAR sensor (Onset Photosynthetically Active Radiation (PAR) Smart Sensor, model S-LIA-M003) deployed on a portable 4-meter tall tripod mast that was set up adjacent to each site during sampling. Data were logged every 1 minute from the time we arrived on site until chamber sampling was completed on an Onset HOBO USB Microstation Logger. When daily sampling was completed, data files were downloaded to a field laptop via HOBOware software (version 3.7.2.1), converted to .csv files, and matched by timestamp to the chamber incubation data via R.

At each chamber sampling location, the three replicate collars were paired with one soil temperature sensor (10 cm depth) and one air temperature sensor (1 m height) mounted on a PVC well in April 2021. Air and soil temperature were logged every 15 minutes. Raw data files were downloaded in the field monthly. Ultimately all data were uploaded as .hobo files to the Woods Hole Coastal and Marine Science Center (WHCMSC) network server. Raw data files were converted to CSV files in the software: HOBOware (version 3.7.2.1). Data were plotted to check for any irregularities in sensor functioning (e.g. outliers or unrealistic values). All found irregularities were removed from the final dataset.

Latitude and longitude of each chamber and sensor location, along with elevation of chambers was measured with a Trimble Real-Time Kinematic (RTK) GPS. Accuracy was 2-3 cm according to instrument corrections. Data files were exported from the instrument via a .csv file and appended to the data files of calculated fluxes or sensors via R.

After all chamber flux data were finalized, we exported the sensor data (logged at 15-minute intervals) that most closely matched the timestamp of the chamber incubation and appended those values to the chamber fluxes data table using R for user convenience. Sensor data included are air and soil temperature described here and availanble in the file air_soil_temp_2021-2022.csv (part of this data release), as well as data on water temperature, water table depth below surface, and salinity, which are available in O'Keefe Suttles and others, 2022.
O'Keefe Suttles, J.A., Eagle, M.J., Sanders-DeMott, R., Nick, S.K., Brooks, T.W., Mann, A.G., and Kroeger, K.D., 2022, Continuous water level, salinity, and temperature data from coastal wetland monitoring wells, Cape Cod, Massachusetts: U.S. Geological Survey data release, https://doi.org/10.5066/P9T1KOTW.