DOI: 10.5061/dryad.xsj3tx9nx
title: Data from: Promoting success in thin layer sediment placement: effects of sediment grain size and amendments on salt marsh plant growth and greenhouse gas exchange

description: Thin layer sediment placement (TLP) is a method to mitigate factors
 resulting in loss of elevation and severe alteration of hydrology, such as
 sea level rise and anthropogenic modifications, and prolong the lifespan
 of drowning salt marshes. However, TLP success may vary due to plant
 stress associated with reductions in nutrient availability and hydrologic
 flushing or through the creation of acid sulfate soils. This study
 examined the influence of sediment grain size and soil amendments on plant
 growth, soil and porewater characteristics, and greenhouse gas exchange
 for three key US salt marsh plants: Spartina alterniflora, Spartina
 patens, and Salicornia pacifica. We found that bioavailable nitrogen
 concentrations (measured as extractable NH4+-N) and porewater pH and
 salinity were found to have an inverse relationship with grain size, while
 soil redox was more reducing in finer sediments. This suggests that
 utilizing finer sediments in TLP projects will result in a more reduced
 environment with higher nutrient availability, while larger grain-sized
 sediments will be better flushed and oxidized. We further found that grain
 size had a significant effect on vegetation biomass allocation and rates
 of gas exchange, although these effects were species-specific. We found
 that soil amendments (biochar and compost) did not subsidize plant growth
 but were associated with increases in soil respiration and methane
 emissions. Biochar amendments were additionally ineffective in
 ameliorating acid sulfate conditions. This study uncovers complex
 interactions between sediment type and vegetation, emphasizing limitations
 of soil amendments. The findings aid restoration project managers in
 making informed decisions regarding sediment type, target vegetation, and
 soil amendments for successful TLP projects.
description: Coastal marsh plant taxa, including <em>Spartina
 alterniflora </em>(synonym <em>Sporobolus
 alterniflorus)</em>,<em> Spartina patens </em>(synonym
 <em>Sporobolus pumilus</em>),<em> </em>and
 <em>Salicornia pacifica</em>,<em> </em>were
 obtained from restoration nurseries (Native West Nursery, San Diego, CA
 & Pinelands Nursery, Columbus, NJ and propagated during the 2018
 growing season in a roof-top greenhouse in Philadelphia, PA (39.9539°,
 -75.1878°) in benthic sediments like those used in thin layer sediment
 placement projects<em>. </em>Plants were tempered over two
 weeks to a final salinity of 20‰, using a mixture of water collected from
 a local marsh at Barnegat Bay, NJ (39.7483°, -74.1931°)
 and distilled water. Plants were exposed to ambient light conditions under
 15% shade cloth, and the greenhouse was outfitted with several fans for
 temperature moderation. Following a 3x4 factorial design replicated four
 times, these three plant species were propagated in four types of
 homogenized sediments of contrasting textures over the course of a growing
 season (130 days; 22 June – 29 Oct 2018). To replicate the way plant plugs
 are planted in the field in restoration projects post sediment
 application,  plugs (5cm x 5cm x 9cm) were obtained from restoration
 nurseries, and those which were relatively homogenous in the amount of
 biomass present were planted into larger containers (10cm x 10cm x
 24cm). Plants were exposed to simulated once-daily
 tides where plants were flooded to a depth of 5 cm for four hours, and the
 soil was drained to 16.5 cm below the sediment surface for twenty hours.
 For reference, this inundation time (17%) corresponds to that considered
 'regularly flooded.' Sediment texture of soil source material
 was analyzed for all sediment types using a laser granulometer (LS 13-320,
 Beckman Coulter, Brea, CA) after pretreatment. Average particle size
 distributions were post-processed with Gradistat.v8 software, including
 bin aggregation to texture classes and statistical description.
 Photosynthesis, community respiration, net ecosystem exchange,
 and methane emissions were measured once from 20 to 29 July 2018 using an
 LGR ultraportable greenhouse gas analyzer (ABB, San José, CA) in a 20L
 chamber. Measurements of net ecosystem exchange were collected during
 five-minute incubations in a transparent chamber, and respiration was
 determined by similar incubations with the chamber covered with black-out
 material. Photosynthesis was calculated as the sum of respiration and net
 ecosystem exchange. The Ideal Gas Law (<em>PV</em> =
 <em>nRT</em>) was used to convert linear changes in
 CO<sub>2</sub> and CH<sub>4</sub> concentrations
 within the chamber during each incubation period to fluxes standardized to
 the surface area of the plant pots. Porewater was
 sampled three times (17 August, 18 September, 24 October 2018), using a
 Rhizon sampler from a depth range of 0-5 cm. Porewater pH was measured
 using a benchtop Thermo Orion A111 pH meter, and porewater salinity was
 measured using a YSI pro30 conductivity and salinity meter. At the end of
 the growing season, aboveground and belowground biomass of the plants was
 determined by harvesting, washing, and drying the plant samples at 60 °C
 to a constant weight. Belowground root material was extracted by washing
 the container sediment over a 2 mm sieve. Soil redox (eH) was measured at
 a depth of 5 cm at harvest using a benchtop Oakton oxidation-reduction
 potential electrode. Sediment samples were collected at harvest and
 processed for KCl extractable ammonium-nitrogen
 (NH<sub>4</sub><sup>+</sup>-N), with ammonium
 concentrations analyzed using the phenate method (EPA Method 350.1; APHA
 2012). Saturated hydraulic conductivity
 (<em>K<sub>sat</sub></em>) was measured (for S1-4)
 using a Decagon KSAT (Decagon Services, Pullman, WA) using the falling
 head method. We conducted short incubation experiments
 to assess the δ<sup>13</sup>C of the
 CO<sub>2</sub> emitted from amended soils to help determine
 whether these emissions could be attributed to plant respiration
 (~δ<sup> 13</sup>C=-16 to -12‰ for C4 grasses) vs.
 remineralization of the carbon in biochar or compost (~δ<sup>
 13</sup>C=-30 to -25‰ associated with C3 plant material). We sampled
 the headspace of the chamber containing plant at the beginning and end of
 30-m incubations using 60 mL luer lock syringes outfitted with a stopcock,
 where the gas was evacuated and stored in 0.1 L Cali-5-bond gas pillows.
 Carbon dioxide was subsequently analyzed for δ<sup>
 13</sup>CO<sub>2</sub> using a benchtop Picarro (Santa
 Clara, CA, USA) G2201i isotope and gas concentration analyzer.
 <em>Biochar and Compost Treatments</em>
 <em>S. alterniflora</em> was grown in coarse sand
 presumed to have low nutrient levels, with and without soil amendments:
 softwood biochar (10% v/v), compost (10% v/v), and with both softwood
 biochar (10% v/v) and compost (10% v/v) to match a paired field study
 (Raposa et al., 2023). Biochar amendments were a commercially available
 softwood biochar (Blacklite Pure, Pacific Biochar, Santa Rosa,
 CA;<em> Pseudotsuga menziesii </em>feedstock). Compost
 feedstock included manure, livestock products, aged pine bark, coir, and
 worm castings (Planting Mix Compost Blend, Organic Mechanics Soil Company,
 Modena, PA). Plants were propagated under identical conditions as the
 first experiment over a growing season (22 June – 29 Oct 2018), with 16
 total units (<em>n</em>=4 per treatment). Plant biomass,
 CO<sub>2</sub> and CH<sub>4</sub> emissions,
 porewater salinity and pH, KCl-extractable
 NH<sub>4</sub><sup>+</sup>-N, and eH measures were
 conducted. Additional samples of <em>S. pacifica
 </em>were grown<em> </em>in two types of benthic
 sediments prone to acidification (S6, S7) with and without a 10% (v/v)
 addition of softwood biochar and without tidal flooding. <em>S.
 pacifica </em>was propagated for 181 days; 22 June – 19 December
 2018. Each treatment was replicated four to six times for a total of 22
 experimental units. As described above, plant total biomass, porewater
 salinity and pH, KCl-extractable
 NH<sub>4</sub><sup>+</sup>-N, and eH were
 measured. In addition, porewater total alkalinity was measured (EPA Method
 2320 B; APHA 2012). <em>Data
 Analysis</em> All statistical analyses were
 performed in R ver. 4.0.3 (R Core Team 2023). Correlation matrices were
 created to examine the dependency of measured variables. The relationship
 between sediment texture and edaphic parameters (eH,
 NH<sub>4</sub><sup>+</sup>-N,
 <em>K<sub>sat</sub></em>, and porewater pH and
 salinity) was tested using a non-parametric Kruskal-Wallis test with
 Bonferroni-correction. Significant interactions
 (<em>p</em>&lt;0.05) were followed by a post hoc
 non-parametric Dunn’s Multiple Comparison Test. To
 determine how sediment texture-related parameters (eH, KCL extractable
 NH<sub>4</sub><sup>+</sup>-N, soil hydraulic
 conductivity, and porewater pH and salinity) drive patterns of plant
 biomass allocation and photosynthesis or CR rates, partial least squares
 regression (PLSR) was performed due to collinearity of predictors. Each
 variable was assessed for variable importance in projection (VIP), where
 VIP scores &gt;1 represent high importance to the regression.
 Bonferroni-corrected one-way Analysis of Variance (ANOVA) tests were run
 to determine differences in sediment grain size effects on plant species’
 biomass and gas emissions, as well as to test if biochar and compost
 treatments on low-nutrient sediments would significantly alter sediment
 eH, NH<sub>4</sub><sup>+</sup>-N, porewater pH,
 and porewater salinity. In certain cases where normality or
 homoskedasticity assumptions could not be met, Kruskal-Wallis tests were
 conducted. Significant effects in the ANOVAs or Kruksal-Wallis tests were
 followed by a post hoc Tukey’s Honestly Significant Difference test or
 Dunn’s Multiple Comparison Tests, respectively. To determine the effects
 of biochar-treatments within non-tidal mesocosms on soil properties (e.g.,
 porewater pH, salinity, eH,
 NH<sub>4</sub><sup>+</sup>-N, and total
 alkalinity), Welch’s Two Sample t-tests were run.
description: # Promoting success in thin layer sediment placement: effects of sediment
 grain size and amendments on salt marsh plant growth and greenhouse gas
 exchange We have presented
 data and code used for data analysis. Data includes data for experiment 1,
 where we analyzed soil and plant traits for plants grown in several
 sediment textures, experiment 2, where we analyzed soil and plant traits
 for plants grown in coarse sand with several soil amendments (biochar,
 compost, biochar and compost), and experiment 3, where we grew plants in
 sediments prone to acidification with and without biochar amendments. ##
 Description of the data and file structure There are three data files
 provided: (1) Experiment1AllData_corrected_CH4.cvs; (2)
 Experiment2AllData.cvs; (3) Experiment3AllData.cvs. ### Experiment 1:
 Where we analyzed soil and plant traits for plants grown in several
 sediment textures Experiment1AllData_corrected_CH4.cvs There are 30 fields
 in this file, consisting of the following column names: bucket, texture,
 Plant, Number, AGBiomass, BGBiomass, TotalBiomass, pH1, pH1Date, pH2,
 pH2Date, pH3, pH3Date,  AvgpH, Sal1, Sal1Date, Sal2, Sal2Date, Sal3,
 Sal3Date, AvgSal, Photosynthesis, Respiration, NEE, ORP, Nutrients,
 NutrientDate, SHC, SHC_dummy, and Methane_L. * bucket - Each mesocosm
 bucket held four plants. Here we report which bucket the plant was in. G1
 = green bucket number 1; G2= green bucket number 2; G3= green bucket
 number 3; R1 = red bucket number 1; R2= red bucket number 2; R3= red
 bucket number 3; B1 = blue bucket number 1; B2= blue bucket number 2; B3=
 blue bucket number 3; Y1 = yellow bucket number 1; Y2= yellow bucket
 number 2; Y3= yellow bucket number 3. * texture - Has one of four fields:
 Fine Sand, Medium Sand, Medium Silt, and Quarry Fines. S1= medium silt;
 S2=fine sand; S3 = quarry fines; S4=medium sand. * Plant - Has one of
 three fields: S. alterniflora, S. pacifica, and S. patens. Each refers to
 the abbreviation for the genus and species name. * Number  - Replicate
 number (1-4). Each species / sediment type combination had four
 replicates. * AGBiomass - The aboveground biomass for each plant pot,
 converted to grams per square meter. * BGBiomass - The aboveground biomass
 for each plant pot, converted to grams per square meter. * TotalBiomass -
 The sum of above and belowground biomass for each plant po, in grams per
 square meter. * pH1 - First porewater pH measurement. * ph1Date - First
 porewater pH measurement date, in MM/DD/YY. If value is impute, the pH1
 measure was a replacement with the mean for the sediment / species
 treatment. * pH2 - Second porewater pH measurement. * pH2Date - Second
 porewater pH measurement date, in MM/DD/YY.  If value is impute, the pH2
 measure was a replacement with the mean for the sediment / species
 treatment. * pH3 - Third porewater pH measurement. * pH3Date - Third
 porewater pH measurement date, in MM/DD/YY.  If value is impute, the pH3
 measure was a replacement with the mean for the sediment / species
 treatment. * AvgpH - Average porewater pH.The average of pH1, pH2, and
 pH3. * Sal1 - First porewater salinity measurement, in parts per thousand.
 * SalDate - First porewater salinity measurement date, in MM/DD/YY. If
 value is impute, the Sal1 measure was a replacement with the mean for the
 sediment / species treatment. * Sal2- Second porewater salinity
 measurement, in parts per thousand. * Sal2Date - Second porewater salinity
 measurement date, in MM/DD/YY. If value is impute, the Sal2 measure was a
 replacement with the mean for the sediment / species treatment. * Sal3-
 Third porewater salinity measurement, in parts per thousand. * Sal3Date -
 Third porewater salinity measurement date, in MM/DD/YY. If value is
 impute, the Sal3 measure was a replacement with the mean for the sediment
 / species treatment. * AvgSal - Average porewater salinity in parts per
 thousand. The average of Sal1, Sal2, and Sal3. * Photosynthesis - The
 difference between net ecosystem exchange and respiration, representing
 photosythesis, measured in micromoles of carbon dioxide per square meter
 per second. Negative values represent CO2 assimilation, and positive
 values indicate net CO2 emissions. * Respiration - Measurement of
 respiration of plant pots in an opaque (dark) chamber in micromoles of
 carbon dioxide per square meter per second. Negative values represent CO2
 assimilation, and positive values indicate net CO2 emissions. * NEE -
 Measurement of net ecosystem exchange of plant pots in a clear chamber in
 micromoles of carbon dioxide per square meter per second. Negative values
 represent CO2 assimilation, and positive values indicate net CO2
 emissions. * ORP - oxidation-reduction potential of soil, measured in
 milivolts (mV). * Nutrients - KCl extractable ammonium, in mg of NH4-N per
 g of dry sediment. * NutrientDate - The date the KCl extractions were
 conducted. * SHC - Saturated hydraulic conductivity of sediment in meters
 per second. Several SHC values were averaged to produce an average measure
 for each sediment type. * SHC_dummy - A dummy variable, where the smallest
 value is the slowest SHC (e.g., in fine sediments), and the largest value
 is the greatest SHC (e.g., in coarse sediments). * Methane_L - Measurement
 of net ecosystem exchange of methane in a clear chamber in micromoles of
 methane per square meter per hour. Negative values represent CH4
 assimilation, and positive values indicate net CH4 emissions. ###
 Experiment 2: Where we analyzed soil and plant traits for plants grown in
 coasrse sand with and without biochar and compost treatments
 Experiment2AllData.cvs There are 29 fields in this file, consisting of the
 following column names: bucket, texture, Plant, Number, AGBiomass,
 BGBiomass, TotalBiomass, pH1, pH1Date, pH2, pH2Date, pH3, pH3Date,  AvgpH,
 Sal1, Sal1Date, Sal2, Sal2Date, Sal3, Sal3Date, AvgSal, NEE, Respiration,
 Photosynthesis, ORP, Nutrients, NutrientDate, and Methane_L, and Dd13C.
 Missing data is denoted by -999. * Bucket - Each mesocosm bucket held four
 plants. Here we report which bucket the plant was in. W1 (raw sand), W2
 (sand with biochar amendments), W3 (sand with compost amendments), and W4
 (sand with biochar and compost amendments). * texture - Has one of four
 fields: Fine Sand, Medium Sand, Medium Silt, and Quarry Fines. S1= medium
 silt; S2=fine sand; S3 = quarry fines; S4=medium sand. * Plant - Has only
 one fields: S. alterniflora, the only plant grown in this experiment. *
 Number  - Replicate number (1-4). Each species / sediment type combination
 had four replicates. * AGBiomass - The aboveground biomass for each plant
 pot, converted to grams per square meter. * BGBiomass - The aboveground
 biomass for each plant pot, converted to grams per square meter. *
 TotalBiomass - The sum of above and belowground biomass for each plant po,
 in grams per square meter. * pH1 - First porewater pH measurement. *
 ph1Date - First porewater pH measurement date, in MM/DD/YY. If value is
 impute, the pH1 measure was a replacement with the mean for the sediment /
 species treatment. * pH2 - Second porewater pH measurement. * pH2Date -
 Second porewater pH measurement date, in MM/DD/YY.  If value is impute,
 the pH2 measure was a replacement with the mean for the sediment / species
 treatment. * pH3 - Third porewater pH measurement. * pH3Date - Third
 porewater pH measurement date, in MM/DD/YY.  If value is impute, the pH3
 measure was a replacement with the mean for the sediment / species
 treatment. * AvgpH - Average porewater pH. The average of pH1, pH2, and
 pH3. * Sal1 - First porewater salinity measurement, in parts per thousand.
 * SalDate - First porewater salinity measurement date, in MM/DD/YY. If
 value is impute, the Sal1 measure was a replacement with the mean for the
 sediment / species treatment. * Sal2- Second porewater salinity
 measurement, in parts per thousand. * Sal2Date - Second porewater salinity
 measurement date, in MM/DD/YY. If value is impute, the Sal2 measure was a
 replacement with the mean for the sediment / species treatment. * Sal3-
 Third porewater salinity measurement, in parts per thousand. * Sal3Date -
 Third porewater salinity measurement date, in MM/DD/YY. If value is
 impute, the Sal3 measure was a replacement with the mean for the sediment
 / species treatment. * AvgSal - Average porewater salinity in parts per
 thousand. The average of Sal1, Sal2, and Sal3. * NEE - Measurement of net
 ecosystem exchange of plant pots in a clear chamber in micromoles of
 carbon dioxide per square meter per second. Negative values represent CO2
 assimilation, and positive values indicate net CO2 emissions. *
 Respiration - Measurement of respiration of plant pots in an opaque (dark)
 chamber in micromoles of carbon dioxide per square meter per second.
 Negative values represent CO2 assimilation, and positive values indicate
 net CO2 emissions. * Photosynthesis - The difference between net ecosystem
 exchange and respiration, representing photosythesis, measured in
 micromoles of carbon dioxide per square meter per second. Negative values
 represent CO2 assimilation, and positive values indicate net CO2
 emissions. * ORP - oxidation-reduction potential of soil, measured in
 milivolts (mV). * Nutrients - KCl extractable ammonium, in mg of NH4-N per
 g of dry sediment. * NutrientDate - The date the KCl extractions were
 conducted. * Methane_L - Measurement of net ecosystem exchange of methane
 in a clear chamber in micromoles of methane per square meter per hour.
 Negative values represent CH4 assimilation, and positive values indicate
 net CH4 emissions. * Dd13C - Change over time in d13C per minute in
 permille (‰). ### Experiment 3: Where we analyzed soil and plant traits
 for plants grown in sediments prone to acidification with and without
 biochar amendments Experiment3AllData.cvs - There are 25 fields in this
 file, consisting of the following column names: bucket, texture, Plant,
 Number, AGBiomass, BGBiomass, TotalBiomass, pH1, pH1Date, pH2, pH2Date,
 pH3, pH3Date,  AvgpH, Sal1, Sal1Date, Sal2, Sal2Date, Sal3, Sal3Date,
 AvgSal, ORP, Nutrients, NutrientDate, and Alkalinity. * Bucket - Each
 mesocosm bucket held four plants. Here we report which bucket the plant
 was in. 1-7. * texture - Has one of four fields: Sand + Pond Mud, Sand +
 Pond Mud + biochar, Wickford, Wickford + biochar. * Plant - Has only one
 field: S. pacifica, the only plant grown in this experiment. * Number  -
 Replicate number (1-6). Each species / sediment type combination had up to
 6 replicates. * AGBiomass - The aboveground biomass for each plant pot,
 converted to grams per square meter. * BGBiomass - The aboveground biomass
 for each plant pot, converted to grams per square meter. * TotalBiomass -
 The sum of above and belowground biomass for each plant po, in grams per
 square meter. * pH1 - First porewater pH measurement. * ph1Date - First
 porewater pH measurement date, in MM/DD/YY. If value is impute, the pH1
 measure was a replacement with the mean for the sediment / species
 treatment. * pH2 - Second porewater pH measurement. * pH2Date - Second
 porewater pH measurement date, in MM/DD/YY.  If value is impute, the pH2
 measure was a replacement with the mean for the sediment / species
 treatment. * pH3 - Third porewater pH measurement. * pH3Date - Third
 porewater pH measurement date, in MM/DD/YY.  If value is impute, the pH3
 measure was a replacement with the mean for the sediment / species
 treatment. * AvgpH - Average porewater pH. The average of pH1, pH2, and
 pH3. * Sal1 - First porewater salinity measurement, in parts per thousand.
 * SalDate - First porewater salinity measurement date, in MM/DD/YY. If
 value is impute, the Sal1 measure was a replacement with the mean for the
 sediment / species treatment. * Sal2- Second porewater salinity
 measurement, in parts per thousand. * Sal2Date - Second porewater salinity
 measurement date, in MM/DD/YY. If value is impute, the Sal2 measure was a
 replacement with the mean for the sediment / species treatment. * Sal3-
 Third porewater salinity measurement, in parts per thousand. * Sal3Date -
 Third porewater salinity measurement date, in MM/DD/YY. If value is
 impute, the Sal3 measure was a replacement with the mean for the sediment
 / species treatment. * AvgSal - Average porewater salinity in parts per
 thousand. The average of Sal1, Sal2, and Sal3. * ORP - oxidation-reduction
 potential of soil, measured in milivolts (mV). * Nutrients - KCl
 extractable ammonium, in mg of NH4-N per g of dry sediment. * NutrientDate
 - The date the KCl extractions were conducted. * Alkalinity - meausured on
 porewater at the end of the experiment (December 2018), as mg per L of
 calcium carbonate (mg/L CaCO3). ## Sharing/Access information None. ##
 Code/Software GH2018Stats.R - ANOVA or non-parametric equivalent for
 "experiment one" (sediment texture vs. response variables). 
 Tests are run for each species, then assumptions are checked, and follow
 up tests conducted. Run on R version 4.3.1 (2023-06-16) using R Studio
 2022.02.1. All packages used are described in the R code.
 GH2018Part2Stats.R - ANOVA or non-parametric equivalent for
 "experiment two" (sediment amendments of biochar and compost). 
 Tests are run for each species, then assumptions are checked, and follow
 up tests conducted. Run on R version 4.3.1 (2023-06-16) using R Studio
 2022.02.1. All packages used are described in the R code.
 GH2018Part3Stats.R - T tests for "experiment three" (sediment
 prone to acidification with and without amendments). Run on R version
 4.3.1 (2023-06-16) using R Studio 2022.02.1. All packages used are
 described in the R code.