Collection, analysis, and age-dating of sediment cores from mangrove wetlands in San Juan Bay Estuary, Puerto Rico, 2016

Five mangrove sites along an urbanization gradient in the San Juan Bay Estuary, Puerto Rico were selected for this study. Sites included the highly urbanized and clogged Caño Martin Peña in the western part of the estuary, a series of lagoons in the center of the estuary, and a tropical forest reserve (Piñones) in the eastern-most part. Mangrove sediment cores, two from each site, about 1 m apart, were collected in March 2016 in the Martin Peña West (MPW), Martin Peña East (MPE), San José Lagoon (SJ), Torrecilla Lagoon (Torr), and Piñones forest (Pin) with a Russian peat sampler to a maximum depth of 50 cm depending upon ability to penetrate coarse mangrove rhizomes. Core depths ranged from 37 – 50 cm. Cores were first covered in saran wrap, then aluminum foil, and then secured with duct tape in a PVC holder for stabilization and transport to the lab. Samples were placed in coolers and shipped to the US mainland via FedEx overnight air transport. Cores were shipped to the USEPA Environmental Effects Research Laboratory, Atlantic Ecology Division in Narragansett, RI. Upon arrival at the lab, the cores were put into the freezer (-18C) until processed.
One core collected from MPW was damaged during air transport to the US mainland and was not radiometrically dated. The other nine cores were sliced in one cm increments at the surface (0 - 3 cm) and then every 2 cm to the bottom of the core (unless otherwise indicated). After slicing, the subsamples were dried in pre-weighed aluminum tins (see subsequent processing steps below). Soil subsamples were used for radiometric dating, stable isotope, percent C, dry bulk density (DBD), and sediment accretion analyses as described below. However, only one of the two replicates from the San José lagoon was processed for DBD due to human error, so DBD values from one SJ core were used in calculations of C storage and sequestration for both replicates from that site.

Sliced subsamples were measured (length, width, and height) and then dried at 60°C for at least 48 hours. The soils were not sieved so the peat included live and decomposing roots. The dried soils were used to determine dry bulk density (gram dry weight divided by volume; g ml-1). A subsample of the dried soil was ground to a fine powder using a mortar and pestle. The dried, ground material was used for stable isotope (C,N) and percent C and N analyses. To remove carbonates, subsamples to be used for %C and C isotope analyses were fumigated prior to analyses with 12 M HCl following the method of Harris and others, 2001. Subsamples for %N and N isotope analyses were not fumigated. The C and N isotope compositions were determined using an Elementar Vario Micro elemental analyzer connected to a continuous flow Isoprime 100 isotope ratio mass spectrometer (IRMS) (Elementar Americas, Mt. Laurel, NJ). Replicate analyses of isotopic standard reference materials USGS 40 (δ13C = -26.39 ‰; δ15N = -4.52 ‰) and USGS 41 (δ13C = 37.63 ‰; δ15N = 47.57 ‰) were used to normalize isotopic values of working standards to the air (δ15N) and Vienna Pee Dee Belemnite (δ13C) scales (Paul and others, 2007). Stable isotope values are expressed in sigma (δ) notation following the formula δX (‰) = [(Rsample / Rstandard) – 1] × 103, where X is the less common isotope and R is ratio of the less common to more common isotope [13C/12C or 15N/14N]. Working standards were analyzed after every 24 samples to monitor instrument performance and check data normalization. The precision of the laboratory standards was better than ± 0.3‰ for δ13C and δ15N. The %C and %N were calculated by comparing the peak area of the unknown sample to a standard curve of peak area versus the C or N content of a known standard.
Harris, D., Horwarth, W.R., and van Kessel, C., 2001, Acid fumigation of soils to remove carbonates prior to total organic carbon or carbon-13 isotopic analysis: Soil Sci. Soc. Am. J. 65:1853–6.
Paul, D., Skrzypek, G. and Fórizs, I., 2007, Normalization of measured stable isotopic compositions to isotope reference scales – A review: Rapid Communications in Mass Spectrometry 21 (18): 3006–3014.

Gamma analysis was performed on 10 to 20 samples that spanned each sediment core. One to ten grams of homogenized sediment were sealed for 3 weeks and counted on a planar-type gamma counter for 24 to 48 hours to measure 137Cs, 210Pb, and 226Ra at 661.6, 46.5 and 352 KeV energies respectively (Canberra Inc. USA). Activities of 137Cs and 210Pb were decay corrected to time of collection; suppression of low energy peaks by self-absorption was corrected according to Cutshall and others, 1983. Age models were developed using Plum (Aquino-López and others, 2018; Blaauw and others, 2020) version 0.1.4 in R version 4.0.0 (R Core Team 2020). Plum is an age-depth model that utilizes 210Pb and is based on the same Bayesian chronology statistical treatment as Bacon, a widely used model with 14C ages (Blaauw and Christen 2011). Plum uses distributions of prior environmental parameters that impact the 210Pb profile, including 210Pb deposition rates, supported 210Pb (i.e., 226Ra) and accretion rates, with posterior distributions providing realistic uncertainty estimates. A major benefit of Plum over the commonly used analytical solution to the continuous rate of supply model (Appleby and Oldfield 1978) is that chronologies can be calculated even if radioisotopes have not been analyzed for the entire core. Furthermore, this model yields more than one accretion rate estimate, unlike the constant initial concentration model (Goldberg, 1963) which is normally used for cores with discontinuous 210PB profiles. Total 210Pb data were input into Plum, with supported 210Pb (i.e., 226Ra) estimated within the model framework from the deepest samples. We broadened the priors from default settings within Plum. We simulated means (50%) and the lower (6%) and upper confidence limits (94%) for each 1 cm depth in the sediment cores. We report means and 88% confidence intervals in the age-depth profiles for each core. Sediment accretion rates (SAR) were obtained from each chronology using the “accrate depth” function in Plum at 1 cm depth intervals.
Cutshall, N.H., Larsen, I.L., and Olsen, C.R., 1983, Direct analysis of 210 Pb in sediment samples—Self-absorption corrections: Nuclear Instruments and Methods in Physics Research, v. 206, issues 1–2, p. 309–312, https://doi.org/10.1016/0167-5087(83)91273-5.
Aquino-López, M.A., Blaauw, M., Christen, J.A., and Sanderson, N.K., 2018, Bayesian analysis of 210 Pb dating: Journal of Agricultural, Biological and Environmental Statistics, v. 23, p. 317–333, https://doi.org/10.1007/s13253-018-0328-7.
Blaauw, M., Christen, J.A., Aquino-López, M.A., Esquivel-Vazquez, J., Gonzalez V., O.M., Belding, T., Theiler, J., Gough, B. and Karney, C., 2020, rplum: Bayesian Age-Depth Modelling of Cores Dated by Pb-210. R package version 0.1.4. https://cran.r-project.org/web/packages/rplum/index.html.
Blaauw, M., and Christen, J.A., 2011. Flexible paleoclimate age-depth models using an autoregressive gamma process: Bayesian Analysis, v. 6, p. 457–474, https://doi.org/10.1214/11-BA618.
Appleby, P.G., and Oldfield, F., 1978, The calculation of lead-210 dates assuming a constant rate of supply of unsupported 210Pb to the sediment: Catena, v. 5, issue 1, p. 1–8, https://doi.org/10.1016/S0341-8162(78)80002-2.
Goldberg, E.D., 1963, Geochronology with 210 Pb, in Miller, J.A., convener, Radioactive dating: International Atomic Energy Agency Symposium on Radioactive Dating, Athens, Greece, November 19-23, 1962, [Proceedings], p. 121-131.

For data in the entity, Data_PR_Cores.csv (and Data_PR_Cores.xlsx), raw data were entered into Excel spreadsheets where calculations for radionuclide decays per minute per gram (dpm/g), dry bulk density, percent carbon, percent nitrogen, and carbon and nitrogen isotope content were completed. Calculations are described in the process steps for each analysis or in each attribute definition. These calculated values were compiled into a CSV file using Microsoft Excel. The CSV file was processed in MATLAB to round calculated values to appropriate place values and truncate extra digits; it was then exported as a comma separated text file (*.csv). Using Microsoft Excel, this exported file was edited to allow for preferential use of special characters and formats, and re-saved as a CSV UTF-8 file, Data_PR_Cores.csv, included in this data release.
The entity, Data_PR_AgeModel.csv, is an output from analysis in R in which we used a bootstrap approach to generate means and 95% confidence bounds for each parameter within cores and specific time periods. The bootstrap analysis generated 1,000 sets of randomly selected data from the reported values for the given core/time period (Efron and Tibshirani 1993). The mean of those 1,000 values was used as the overall mean estimate for the parameter, and the 2.5th and 97.5th percentiles of those 1,000 values were the upper and lower confidence bounds. We report age means and 95% confidence intervals in the age-depth profiles for each core and use these estimates to calculate accretion rates. This file is saved as csv UTF-8.
Note that all calculations were performed prior to rounding and truncating values reported in this data release. Microsoft Excel (*.xlsx) versions of each entity are provided for users to verify proper text formatting that may not be preserved when opening the .csv files in certain editors.
Efron, B., and Tibshirani, R.J., 1993, An Introduction to the Bootstrap. Boca Raton, FL: Chapman and Hall/CRC.