Static chamber fluxes of carbon dioxide and methane from Phragmites wetlands and supporting data collected across a salinity gradient on Cape Cod, Massachusetts

Four sampling locations were established across a salinity gradient for static chamber sampling. Two sampling locations were established at a site with natural, unrestricted tidal exchange at Sage Lot Pond in a high (Unrestricted-High; mean 2020 salinity of ~25) and low (Unrestricted-Low; mean 2020 salinity of ~12) salinity location relative to the site and two were established at the impounded Herring River in a high (Impounded-High; mean 2020 salinity of ~9) and low (Impounded-Low; mean 2020 salinity of ~4) salinity location relative to the site. Each sampling location was equipped with three replicate collars for static chamber measurements and one pair of air/soil temperature sensors. In addition, data from a 3m tall mast at Sage Lot Pond equipped with sensors to measure relative humidity, temperature, and photosynthetically active radiation (PAR) are included.
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 = 4)) were inserted into the sediment surrounding intact vegetation to a depth of at least 10 cm more than four weeks prior to initial sampling. 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 m tall. Depending on the height of the vegetation at the sampling location we used either two (unrestricted sites at Sage Lot Pond) or three (impounded sites at Herring River) stacked chambers for a total chamber height of 1.83 or 2.74 m and empty chamber volume of 0.43 or 0.64 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 3-7 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 150-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. One measurement did not have a slope significantly different than 0, and that flux was therefore set to 0.
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.

A survey of live Phragmites culm density, along with mean height and diameter was conducted in early September 2020 prior to senescence. We established five evenly spaced 1 m2 quadrats around both a 4 m and 8 m radius circle centered on the center point of the sampling location between the chambers using a meter tape and a compass (n = 10 per quadrats per site). From the center point of the chambers, we used a compass to determine the direction of 0, 72, 144, 216, and 288 degrees offset from North (azimuth) and then used a meter tape to measure out 4 m or 8 m along each of those compass readings. We placed a flag at the 4 or 8 m mark and then used a 1 square meter pvc square to delineate the border of the quadrat. Within each quadrat we counted live stems, measured the height of culms with a meter tape, and measured the diameter of culms at 50cm height with a calliper. Measurements were recorded on a field data sheet and later entered into an electronic spreadsheet and mean values for height and diameter were calculated for each quadrat. Dry biomass was calculated using both height and diameter according to a Phragmites-specific allometric equation (Lu and others, 2016).
Lu, M., Caplan, J.S., Barker, J.D., Langley, J.A., Mozdzer, T.J., Drake, B.G., and Megonigal, J.P., 2016, Allometry data and equations for coastal marsh plants: Ecology, 97(12), 3554. https://doi.org/10.1002/ecy

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.

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 June 2020. Air and soil temperature were logged every 15 minutes. Raw data files were downloaded in the field monthly. Ultimately all data was 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). Each deployment file was uploaded into R-studio. Data was then checked for completeness by creating a proxy timeseries specific to each collected dataset, timestamp values that were not collected were replaced by blank cell values. Data were plotted to check for any irregularities in sensor functioning. All found irregularities were removed from the final dataset. Data from Sage Lot Pond are included from July 1, 2020 through December 31, 2020 and data from Herring River are included from July 1, 2020 through April 22, 2021.

At Sage Lot Pond, near the Unrestricted-High sampling location we installed an aluminum mast equipped with sensors to measure above canopy air temperature and relative humidity (Onset HOBO Temperature/RH Smart Sensor S-THB-M00x, Bourne, MA, USA enclosed in a radiation shield) and incoming photosynthetically active radiation (PAR; Onset HOBO Photosynthetically Active Radiation Smart Sensor S-LIA-M003, Bourne, MA, USA). The system was set up to log data every 15 minutes. Raw data files were downloaded in the field monthly. Ultimately all data was 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). Each deployment file was uploaded into R-studio. Data were then checked for completeness by creating a proxy timeseries specific to each collected dataset, timestamp values that were not collected were replaced by blank cell values. Data was plotted to check for any irregularities in sensor functioning. All found irregularities were removed from the final data set. Data from Sage Lot Pond are included from July 1, 2020 through December 31, 2020.

Metadata file was updated to reflect a revision to the larger data release, although data tables described here are unchanged in version 2. Cross references for journal publication and related data release were also added, along with minor corrections of typos and census unit of site locations. The related data release (O'Keefe Suttles and others, 2022) provides time series data from well sensors at each of the sites during the time period of the measurements published here.
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.