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opencc-by-4.0Aug 2021View details →

Biogeomorphic modeling to assess the resilience of tidal-marsh restoration to sea level rise and sediment supply - Supporting code and data

Code and data to reproduce figures and analyses of the paper: Gourgue, O., van Belzen, J., Schwarz, C., Vandenbruwaene, W., Vanlede, J., Belliard, J.-P., Fagherazzi, S., Bouma, T.J., van de Koppel, J., and Temmerman, S.: Biogeomorphic modeling to assess resilience of tidal marsh restoration to sea level rise and sediment supply, Earth Surf. Dynam., submitted. Standard Python dependencies: <ul> <li>GDAL</li> <li>Geopandas</li> <li>Matplotlib</li> <li>NumPy</li> <li>Rasterio</li> <li>SciPy</li> <li>Seaborn</li> <li>Shapely</li> <li>scikit-learn</li> </ul> Third-party Python dependencies: <ul> <li>Centerline (https://github.com/fitodic/centerline)</li> <li>pputils (https://github.com/pprodano/pputils)</li> <li>pysheds (https://github.com/mdbartos/pysheds)</li> </ul> In-house Python dependencies: <ul> <li>Demeter 1.0.5 (https://doi.org/10.5281/zenodo.5205258)</li> <li>OGTools 1.1 (https://doi.org/10.5281/zenodo.3994952)</li> <li>TidalGeoPro 0.1 (https://doi.org/10.5281/zenodo.5205285)</li> </ul>

opencc-by-4.0Jul 2019View details →

Fig. 3 in Size-At-Age Variability And Sexual Dimorphism Of Morphometric Characteristics In The Late Ontogenesis Of The Marsh Frog, Pelophylax Ridibundus (Anura, Ranidae), From Terrytory Of Crimea

Fig. 3. The differentiation of males (А) and females (B) of the marsh frog according to the absolute values of the body measurements.

opencc-by-4.0Jul 2019View details →

Fig. 2 in Size-At-Age Variability And Sexual Dimorphism Of Morphometric Characteristics In The Late Ontogenesis Of The Marsh Frog, Pelophylax Ridibundus (Anura, Ranidae), From Terrytory Of Crimea

Fig. 2. Micrographs of cross- sections through the middle part of the diaphysis of the fifth phalange of the fourth toe of frogs: a, b, c, d, e — the arrow indicates the lines that correspond wintering 1–5.

opencc-by-4.0Apr 2022View details →

Methane fluxes from four elevation zones in a St. Lawrence Estuary salt marsh

Dataset used in <a href="https://iopscience.iop.org/article/10.1088/2752-664X/ac706a/meta">Spartina alterniflora has the highest methane emissions in a St. Lawrence estuary salt marsh - IOPscience</a>. The dataset contains methane fluxes calculated from gas measurements taken over a 40 or 60 minute period using a dark static chamber method. Methane fluxes were measured at six locations in four elevation zones of a northern salt marsh on the St. Lawrence River estuary at La Pocatière, Quebec (47°22'24.7"N 70°03'26.3"W). Additional environmental data was collected including carbon dioxide fluxes, extractable soil nitrate, extractable soil ammonium, extractable soil dissolved organic carbon, extractable soil total dissolved nitrogen, salinity, temperature, water table depth, soil total organic carbon, soil total nitrogen, soil organic carbon to nitrogen ratio and bulk density. Soil cores were collected from 0-15 cm and used for extractable nutrient analysis, bulk density and soil organic carbon and nitrogen analysis. The work was carried out with funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement 838296, a NSERC Discovery Grant and a Natural Environment Research Council grant number (NE/T012323/1). This dataset is used in a publication entitled Spartina alterniflora has the highest methane emissions in a St. Lawrence Estuary salt marsh in Environmental Research: Ecology (https://doi.org/10.1088/2752- 664X/ac706a), which also contains more details on fieldsite and methodology. Gas samples were collected from dark, static chambers (18L, 26 cm diameter), which were placed onto pre-inserted collars in the vegetated zones (inserted to 2.5 cm, 3 days prior to sampling) or placed directly onto the mudflat. The chambers were insulated and fitted with fans and venting tubes. Gas samples were collected on the 23rd August 2020 from all sites, soil cores were collected between the 24-25th August 2020 and the 19-20th September 2020. Soil samples were collected at 0-15 cm using a 2.5 cm diameter dutch gouge corer. Soil temperature was measured at 10 cm depth using a soil thermometer, (°C, DeltaTrak 11050, Pleasanton, USA), salinity was measured in the laboratory using a portable ATC refractometer. Water table depth was measured using a PVC piezometer, a plastic pipe with tubing was inserted into the piezometer and blown into to determine water table depth through bubbling sound (cm). Soil cores were dried at 60 °C to constant weight and the dry weight over core volume used to calculate bulk density (g cm-3), soil was finely ground and analysed for total organic carbon and total nitrogen (%) using an Elemental Analyser (ThermoFinnigan Flash EA 1112 CN analyser, Carlo Erba, Milan, Italy) with an accuracy of ±5 % for N and ±1 % for C, and a limit of 171 detection of 0.05 % for both N and C. Extractable nitrate+nitrite (assumed to be nitrate) were analysed in soil extractant (2M KCl, 5:1 of extractant to soil) using a microplate reader and methods in Sims et al., 1995 (<a href="https://doi.org/10.1080/00103629509369298">https://doi.org/10.1080/00103629509369298</a>) with a limit of detection of 0.1 ppm and accuracy of ±5%. Extractable dissolved organic carbon and total dissolved nitrogen were analysed in soil extractant (ultrapure water 18.2 MΩ, 5:1 of extractant to soil) on a TOC/TDN analyser (TOC VCSn + TMN-1, Shimadzu, Kyoto, Japan), with a 50 mg C l -1 standard resulting in an accuracy and precision of 3.0 and ±4.4 mg l-1, respectively. CH4 and CO2 concentrations were measured in the gas samples using a gas chromatograph (GC-14, Shimadzu, Kyoto, Japan) fitted with a flame ionisation detector, CO2 was methanised to CH4 before analysis. Standards of CH4 (5.1 ppm) and CO2 (5000 ppm) resulted in an accuracy and precision of 6.6±1.5 and 0.4 ppm, and 5324±324 and 78 ppm, respectively, for CH4 and CO2. Changes in gas concentration over time were converted to fluxes using a linear regression of the linear portion fo the flux and if fluxes were below the minimum detectable concentration difference (see <a href="https://doi.org/10.1002/2017JG003783">https://doi.org/10.1002/2017JG003783</a>), they were set to zero. Results from the experiments were entered into an Excel spreadsheet for ingestion into the Zenodo data repository.

dryad40/100

Using marsh organs to test seed recruitment in tidal freshwater marshes

Premise: Seed recruitment niches along estuarine elevation gradients are seldom experimentally field-tested under tidal regimes of the Pacific Northwest of North America. Addressing this knowledge gap is important to better understand estuary restoration and plant community response to sea level rise. Methods: Germination was tested in marsh organ mesocosms across an elevation gradient (0.5–1.7 m above mean sea level). Seeds were sown on sterile peat moss, and the tops of pipes were secured with horticultural "frost cloth" to ensure no experimental seeds were washed out and no new seeds were introduced. The trials tested artificial and overwinter chilling regimes, as well as the presence and/or absence of a near-neighbor transplant. Results: Carex lyngbyei had significant elevation-driven germination after overwinter and artificial chilling. Schoenoplectus tabernaemontani had near-significant germination across elevation after overwinter chilling, and germination in the absence of competition was significantly greater than with a near-neighbor transplant. Discussion: Carex lyngbyei had the highest germination rate at higher elevations, which suggests restricted seed recruitment potential, and required clonal expansion to extend into lower marsh elevations. Identifying species-specific recruitment niches provides insight for restoration opportunities or invasive species monitoring, as well as for estuary migration under sea level rise.

opencc-zeroDec 2021View details →

opencc-by-4.0Sep 2022View details →

Data from: Increasing tidal inundation corresponds to rising porewater nutrient concentrations in a southeastern U.S. salt marsh

Salt marshes are ecologically and economically important features of coastal environments that are vulnerable to sea level rise, the rate of which has accelerated in recent decades along the southeastern US Atlantic coast. Increased flooding frequency and duration across the marsh platform is predicted to impact vegetation community structure and overall marsh persistence, but the effect of changing inundation patterns on biogeochemical processes in marsh sediments remains largely unexplored. As part of a long-term monitoring effort to assess how marshes are responding to sea level rise in North Inlet estuary (South Carolina, USA), we collected data on porewater nutrient concentrations from a series of permanent monitoring plots across multiple transects spanning the marsh elevation gradient during the growing season from 2009 to 2019. Additionally, we calculated time inundated for each plot using local water level data and high-resolution elevation measurements to assess the change in time flooded at each plot. Our results indicate that both NH4 and PO4 nutrient concentrations have increased in most permanent plots over the 11-year study period and that nutrient concentrations are higher with increasing proximity to the creek. Spatial patterns in nutrient increases through time are coincident with considerable increases in tidal inundation observed over the marsh platform. Across plots located in the low marsh, porewater NH4 and PO4 concentrations have risen at average rates of 8.96 µM/year and 0.86 µM/year, respectively, and have reached rates as high as 27.25 µM/year and 3.13 µM/year. We suggest that increased inundation time due to rising sea level has altered biogeochemical conditions influencing nutrient availability in marsh porewater, resulting in increases that likely have relevance for larger scale nutrient cycles as well as marsh ecosystem stability and function.

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Diversity and composition of macroinvertebrate communities in a rare inland salt marsh

Inland salt marshes are rare habitats in the Great Lakes region of North America, formed on salt deposits from the Silurian period. These patchy habitats are abiotically stressful for the freshwater invertebrates that live there, and provide an opportunity to study the relationship between stress and diversity. We used morphological and COI metabarcoding data to assess changes in diversity and composition across both space (a transect from the salt seep to an adjacent freshwater area) and time (three sampling seasons). Richness was significantly lower at the seep site with both datatypes, while metabarcoding data additionally showed reduced richness at the freshwater transect end, consistent with a pattern where intermediate levels of stress show higher diversity. We found complementary, rather than redundant, patterns of community composition using the two datatypes: not all taxa were equally sequenced with the metabarcoding protocol. We identified taxa that are abundant at the salt seep of the marsh, including biting midges (Culicoides) and ostracods (Heterocypris). We conclude that (as found in other studies) molecular and morphological work should be used in tandem to identify the biodiversity in this rare habitat. Additionally, salinity may be a driver of community membership in this system, though further ecological research is needed to rule out alternate hypotheses.

opencc-zeroOct 2022View details →

opencc-by-4.0Oct 2022View details →

Data from: Sedimentary organic carbon and nitrogen sequestration across a vertical gradient on a temperate wetland seascape including salt marshes, seagrass meadows and rhizophytic macroalgae beds

Dataset    Coastal wetlands are key in regulating coastal carbon and nitrogen dynamics and contribute significantly to climate change mitigation and anthropogenic nutrient reduction. We investigated organic carbon (OC) and total nitrogen (TN) stocks and burial rates at four adjacent vegetated coastal habitats across the seascape elevation gradient of Cádiz Bay (South Spain), including one species of salt marsh, two of seagrasses, and a macroalgae. OC and TN stocks in the upper 1 m sediment layer were higher at the subtidal seagrass Cymodocea nodosa (72.3 Mg OC ha-1, 8.6 Mg TN ha-1) followed by the upper intertidal salt marsh Sporobolus maritimus (66.5 Mg OC ha-1, 5.9 Mg TN ha-1), the subtidal rhizophytic macroalgae Caulerpa prolifera (62.2 Mg OC ha-1, 7.2 Mg TN ha-1), and the lower intertidal seagrass Zostera noltei (52.8 Mg OC ha-1, 5.2 Mg TN ha-1). The sedimentation rates increased from lower to higher elevation, from the intertidal salt marsh (0.24 g cm-2 yr-1) to the subtidal macroalgae (0.12 g cm-2 yr-1). The organic carbon burial rate was highest at the intertidal salt marsh (91 ± 31 g OC m-2 yr-1), followed by the intertidal seagrass, (44 ± 15 g OC m-2 yr-1), the subtidal seagrass (39 ± 6 g OC m-2 yr-1), and the subtidal macroalgae (28 ± 4 g OC m-2 yr-1). Total nitrogen burial rates were similar among the three lower vegetation types, ranging from 5 ± 2 to 3 ± 1 g TN m-2 yr-1, and peaked at S. maritimus salt marsh with 7 ± 1 g TN m-2 yr-1. The contribution of allochthonous sources to the sedimentary organic matter also decreased with elevation, from 72% in C. prolifera to 33% at S. maritimus. Our results highlight the need of using habitat-specific OC and TN stocks and burial rates to improve our ability to predict OC and TN sequestration capacity of vegetated coastal habitats at the seascape level. We also demonstrated that the stocks and burial rates in C. prolifera habitats were within the range of well-accepted blue carbon ecosystems such as seagrass meadows and salt marshes.

opencc-by-4.0May 2024View details →

Dataset: Blue carbon dynamics across a salt marsh-seagrass ecotone in a cool-temperate South African estuary

This is a dataset of organic carbon, nitrogen, and phosphorus content from the Olifants estuary. The study was designed to investigate drivers of variability at different spatial scales and across the salt marsh-seagrass ecotone. Samples were collected in March 2023 from three selected sites (upper, middle, and lower) in the estuary. Each site featured three transects, extending from the salt marsh vegetation of mixed species through the Zostera capensis seagrass meadows towards the water. Sediment cores were taken to a depth of 50 cm, but only the top 0-5 cm section was analyzed. Carbon and nitrogen content were measured using an Elementar Vario EL Cube Elemental CHNS Analyzer, while phosphorus was determined by ICP at Central Analytical Facilities  (Stellenbosch University).   <table> <tbody> <tr> <td> Sampling site </td> <td> GPS coordinates </td> </tr> <tr> <td> Upper </td> <td> 31°39'45.27"S, 18°11'42.40"E </td> </tr> <tr> <td> Middle </td> <td> 31°40'56.46"S, 18°12'3.72"E </td> </tr> <tr> <td> Lower </td> <td> 31°41'39.85"S, 18°11'15.95"E </td> </tr> </tbody> </table>   File description CHNS_Dataset_SM&INT.xlsx: Data for intermediate sample measurements including percent organic carbon content and and percent nitrogen content for all sites ICP_Data_INT.xlsx: Data for Phosphorus content and other related measurements for the upper site.

Fig. 6 in The aquatic Heteroptera (Hemiptera) of marshes in the Florida Everglades

Fig. 6. Illustrations of the color patterns on the head and thorax of the 2 adult female individuals of Trepobates floridensis found in Everglades marsh samples. (a, b) are dorsal illustrations and (c, d) are lateral illustrations; (a, c) are of the individual from the Panhandle region on 5 Jul 2017; (b, d) are of the individual from northeastern Everglades National Park on 19 Sep 2016. Corresponding photographs are in the supplements (Figs. S5, S6).

Fig. 3 in The aquatic Heteroptera (Hemiptera) of marshes in the Florida Everglades

Fig. 3. Adult density (number of individuals per m2) maps of the 2 species of Belostomatinae, (a, b) Abedus immaculatus and (c, d) Belostoma lutarium, from Modified Water Delivery (lef column) during water yr 2017 and Comprehensive Everglades Restoration Plan samples (right column) during 2016 and 2017. Each point represents 1 sample site (Modified Water Deliveries) or primary sampling unit (Comprehensive Everglades Restoration Plan). Regions are labeled in (a). Regions: ENP = Everglades National Park; LOX = Loxahatchee National Wildlife Refuge; PHD = Everglades National Park panhandle; SRS = Shark River Slough; TSL = Taylor Slough; UTS = Upper Taylor Slough; WCA = Water Conservation Areas.

Fig. 5 in The aquatic Heteroptera (Hemiptera) of marshes in the Florida Everglades

Fig. 5. Density maps (number of individuals per m2) of Negerris hesione in (a) Modified Water Delivery during water yr 2017 and (b) Comprehensive Everglades Restoration Plan samples during 2016 and 2017; (c) density (number of individuals per m2) of N. hesione by region in Modified Water Deliveries samples by sampling period. Sampling periods represented encompass all of water yr 2017 from the start of the wet season (Jul 2016; period 1) to the end at the start of the dry (Apr 2017; period 5); see Table 1. Regions: LOX = Loxahatchee National Wildlife Refuge; PHD = Everglades National Park panhandle; SRS = Shark River Slough; TSL = Taylor Slough; WCA = Water Conservation Areas. Shaded area represents the wet season; unshaded area is the dry season.

Fig. 2 in The aquatic Heteroptera (Hemiptera) of marshes in the Florida Everglades

Fig. 2. Density (number of individuals per m2) of Pelocoris balius (lef column) and Pelocoris femoratus (right column) by region in Modified Water Delivery samples by sampling period and life stage: (a, b) adult females; (c, d) adult males; (e, f) nymphs. Sampling periods represented encompass all of water yr 2017 from the start of the wet season (Jul 2016; period 1) to the end at the start of the dry (Apr 2017; period 5); see Table 1. Regions: PHD = Everglades National Park panhandle; SRS = Shark River Slough; TSL = Taylor Slough; WCA = Water Conservation Area 3. Shaded areas represent the wet season; unshaded areas are the dry season.

Fig. 1 in The aquatic Heteroptera (Hemiptera) of marshes in the Florida Everglades

Fig. 1. Adult density (number of individuals per m2) maps of the 3 species of Pelocoris by project. The top row is Modified Water Delivery samples during water yr 2017, whereas the bottom row is Comprehensive Everglades Restoration Plan samples during 2016 and 2017. Each point represents 1 sample site (Modified Water Deliveries) or primary sampling unit (Comprehensive Everglades Restoration Plan). Regions are labeled in (a). No P. carolinensis were collected in Modified Water Deliveries samples. Regions: ENP = Everglades National Park; LOX = Loxahatchee National Wildlife Refuge; PHD = Everglades National Park panhandle; SRS = Shark River Slough; TSL = Taylor Slough; UTS = Upper Taylor Slough; WCA = Water Conservation Areas.

Fig. 4 in The aquatic Heteroptera (Hemiptera) of marshes in the Florida Everglades

Fig. 4. Density (number of individuals per m2) of species of Belostomatinae by region in Modified Water Deliveries samples by sampling period: (a) Abedus immaculatus, (b) Belostoma lutarium, (c) combined nymphs of both species. Sampling periods represented encompass all of water yr 2017 from the start of the wet season (Jul 2016; period 1) to the end at the start of the dry season (Apr 2017; period 5); see Table 1. Regions: PHD = Everglades National Park panhandle; SRS = Shark River Slough; TSL = Taylor Slough; WCA = Water Conservation Area 3. Shaded areas represent the wet season; unshaded areas are the dry season.

opencc-by-4.0Oct 2023View details →

Roy Tsuda, Jeanine Olsen and Jim Marsh (Wytze Stam back center) lunching and reminiscing at The Hau Tree, Kaimana Beach, Hawaii in 2011. in Tribute to Roy Toshio Tsuda (1939 - 2020)

Roy Tsuda, Jeanine Olsen and Jim Marsh (Wytze Stam back center) lunching and reminiscing at The Hau Tree, Kaimana Beach, Hawaii in 2011.

Fig. 4 in Mosaic Structure Of Ant Communities (Hymenoptera: Formicidae) In Eastern Carpathian Marshes: Regional Versus Local Scales

Fig. 4. Number of Myrmica ruginodis specimens in the absence (1), and in the presence (2) of M. rubra (Mann–Whitney U–test, z = –5.14, p <0.000, n1 = 29, n2 = 74)

Fig. 2 in Mosaic Structure Of Ant Communities (Hymenoptera: Formicidae) In Eastern Carpathian Marshes: Regional Versus Local Scales

Fig. 2. The overall evenness vs. the evenness of the mean patch–diversity values for each sample site (V – Voslobeni, LD – Lacul Dracului, FR – Fagul Rotund, AL – Apa Lenta)

Fig. 3 in Mosaic Structure Of Ant Communities (Hymenoptera: Formicidae) In Eastern Carpathian Marshes: Regional Versus Local Scales

Fig. 3. Number of Myrmica rubra specimens in the absence (1), and in the presence (2) of M. ruginodis (Mann–Whitney U–test, z = –5.15, p <0.000, n1 = 47, n2 = 56)

Fig. 1 in Mosaic Structure Of Ant Communities (Hymenoptera: Formicidae) In Eastern Carpathian Marshes: Regional Versus Local Scales

Fig. 1. PCoA–plot of the ant–communities, each dot representing a single trap: filled dots – open peat–bog habitats with sparse trees; empty dots – sedge meadows; crosses – marshland forests; A –