Data from: Burrowing crab effects on the properties and functions of coastal soft sediments

Rinehart, Shelby 1

Research facility: University of Alabama

Published Apr 29, 2024 on Dryad. https://doi.org/10.5061/dryad.3bk3j9kt3

Data files

Apr 29, 2024 version files 830.71 KB

README.md

11.02 KB
Rinehart_et_al.202X_Effectsizes.csv

533.90 KB
Rinehart_et_al.202X_PublicationBias.csv

285.79 KB

Abstract

Burrowing ecosystem engineers, such as termites, crabs, marmots, and foxes, can profoundly affect the biological structure and ecosystem functions of their environments. However, the relative importance of burrowing engineers on sediments are challenging to predict and are expected to be influenced by engineer density, engineer functional traits (e.g., burrow morphology), and environmental conditions (e.g., geomorphology, vegetation presence). To develop robust hypotheses predicting the impacts of burrowing ecosystem engineers, we conducted a systematic meta-analysis evaluating the effects of burrowing crabs on sediment properties, nutrient stocks, and ecosystem functions in coastal soft-sediment habitats (e.g., salt marshes, mangrove forests, tidal flats). The data set includes 1422 effect size calculations for the effects of burrowing crabs on sediments collected from 59 total manuscripts. The data suggest that burrowing crabs rework and oxygenate sediments and accelerate rates of nutrient cycling (i.e., nitrification and CO₂ flux). However, the magnitude and direction of burrowing crab effects depend on burrowing crab superfamily, the presence of vegetation, and their interaction. Crab burrow density does not consistently predict burrowing engineer effects on sediments.

https://doi.org/10.5061/dryad.3bk3j9kt3

Effect size calculations (including means, sample sizes, and standard deviation) of crab burrowing effects (i.e., high density vs low density) on the properties, nutrient stocks, and functions of coastal sediments. Data comes from studies conducted across Africa, Asia, Australia, North America, and South America.

Description of the data and file structure

File list:

Rinehart_et_al.202X_Effectsizes

CSV file containing the Hedges d effect size calculations (including the raw means, sample sizes, and standard deviations) for each extracted comparison/study from all 59 manuscripts. Additional extracted data (e.g., crab taxa, experimental conditions, habitat, burrow density) are also included for each comparison/study.
Rinehart_et_al.202X_Publicationbias

CSV file containing the pooled standard deviation and the Hedges d effect size calculation for each comparison/study. This datafile was used to conduct analyses of publication bias for a resulting systematic meta-analysis.

Data-specific information for: (1) Rinehart_et_al.202X_Effectsizes

Number of variables: 47

Number of cases/rows: 1423

Variable List:

id: the unique code assigned to each data row.
reference: author, year, and journal for each data source.
pub_year: year of reference publication. One in preparation study was included in the dataset (Rinehart et al. 20XX), it's publication year is denoted as 20XX.
paper id: the unique code assigned to each manuscript included in the dataset.
continent: the continent where the data was collected.
country: the country where the data was collected.
state: the state (united states only) where the data was collected.
estuary: the name of the estuary where the data was collected.
latitude_dd: the latitude associated with the data collected in decimal degrees (dd).
longitude_dd: the longitude associated with the data collected in decimal degrees (dd).
ecosystem: the type of ecosystem (e.g., salt marsh, mangrove forest, tidal flat) associated with the collected data.
vegetation: categorical variable noting the presence (vegetated) or absence (not unvegetated) of any vegetation.
ecosystem_type: categorical variable noting if the ecosystem was restored, created, or natural.
relative_salinity: categorical variable noting the relative salinity in the ecosystem where the data was collected.
tidal_amplitude_m: the tidal amplitude (in meters) in the ecosystem where the data was collected.
tidal_cycle: categorical variable noting the type of tidal cycle (e.g., diurnal) in the ecosystem where the data was collected.
soil_type: categorical variable noting the soil type (e.g., sand) in the ecosystem where the data was collected.
elevation_m: the elevation (in meters) of the ecosystem where the data was collected.
study_duration_d: the length of time (in days) that the study ran (applies mainly to manipulative studies).
study_timing: the seasons or months during which the study was run.
dominant_plant_genus: the genus of the dominant plant present in the ecosystem where the data was collected.
dominant_plant_species: the species of the dominant plant present in the ecosystem where the data was collected.
dominant_plant_functional_group: categorical variable noting the functional group (e.g., grass) of the dominant plant species in the ecosystem where the data was collected.
crab_genus: the genus of the dominant burrowing crab used in the study. Studies with mixed crab communities are denoted with by "mixed".
crab_species: the species of the dominant burrowing crab used in the study. Studies with mixed crab communities are denoted with by "mixed".
crab_diet: categorical variable noting the main feeding strategy (e.g., herbivore, detritivore) used by the dominant crab species.
crab_superfamily: the superfamily of the dominant burrowing crab used in the study. Studies with mixed crab communities are denoted with by "mixed".
mean_burrow_diameter_high_crab_treatment_mm: the mean burrow diameter in the study's high crab treatment in mm.
mean_burrow_diameter_low_crab_treatment_mm: the mean burrow diameter in the study's low crab treatment in mm.
mean_burrow_depth_cm: the mean burrow depth in cm reported by the study.
burrow_density_high_crab_m^2: the mean crab burrow density per meter-squared reported in the study's high crab treatment.
burrow_density_low_crab_m^2: the mean crab burrow density per meter-squared reported in the study's low crab treatment.
experiment_type: categorical variable noting if the study used observational or manipulative methodologies.
experiment_setting: categorical variable noting if the study was conducted in a laboratory or field setting. Laboratory studies also include outdoor mesocosm studies.
field_location: categorical variable noting where studies conducted in the field placed their study relative to the shoreline. Specifically, we noted if studied sampled in the ecosystem interior (far from shoreline) or at the ecosystem edge (adjacent to the shoreline).
soil_depth_cm: the depth, in cm, within the soil profile from which the sediment samples were collected.
soil_characteristic_measured: categorical variable identifying the specific sediment property, nutrient stock, or function that was quantified by the study.
soil_characteristic_units: the original units used to quantify the soil characteristic within the study.
mean_low_crab: the mean value of the soil characteristic measured in the low crab treatment within the study.
sd_low_crab: the standard deviation of the soil characteristic measured in the low crab treatment within the study.
n_low_crab: the sample size of the soil characteristic measured in the low crab treatment within the study.
mean_high_crab: the mean value of the soil characteristic measured in the high crab treatment within the study.
sd_high_crab: the standard deviation of the soil characteristic measured in the high crab treatment within the study.
n_high_crab: the sample size of the soil characteristic measured in the high crab treatment within the study.
crab_density: categorical variable noting if the study documented relative burrowing crab density within their study using burrow density (burrow) or counts of individuals (individuals).
hedges_d: the hedges d effect size calculated for the effects of burrowing crabs on the measured sediment characteristic. Hedges d values were calculated in OpenMee software (see code/software below). Positive effect sizes indicate that burrowing crabs increased the value of the sediment measurement, while negative effect sized indicate that burrowing crabs decreased the value of the sediment measurement.
hedges_d_var: the variation of the hedges d effect size calculated for the effects of burrowing crabs on the measured sediment characteristic. Hedges d variation values were calculated in OpenMee software (see code/software below).

Missing data codes: na

Data-specific information for: (2) Rinehart_et_al.202X_Publicationbias

Number of variables: 22

Number of cases/rows: 1423

Variable List:

id: the unique code assigned to each data row.
reference: author, year, and journal for each data source.
pub_year: year of reference publication. One in preparation study was included in the dataset (Rinehart et al. 20XX), it's publication year is denoted as 20XX.
paper id: the unique code assigned to each manuscript included in the dataset.
ecosystem: the type of ecosystem (e.g., salt marsh, mangrove forest, tidal flat) associated with the collected data.
vegetation: categorical variable noting the presence (vegetated) or absence (not unvegetated) of any vegetation.
crab_superfamily: the superfamily of the dominant burrowing crab used in the study. Studies with mixed crab communities are denoted with by "mixed".
burrow_density_high_crab_m^2: the mean crab burrow density per meter-squared reported in the study's high crab treatment.
experiment_type: categorical variable noting if the study used observational or manipulative methodologies.
experiment_setting: categorical variable noting if the study was conducted in a laboratory or field setting. Laboratory studies also include outdoor mesocosm studies.
soil_characteristic_measured: categorical variable identifying the specific sediment property, nutrient stock, or function that was quantified by the study.
soil_characteristic_units: the original units used to quantify the soil characteristic within the study.
mean_low_crab: the mean value of the soil characteristic measured in the low crab treatment within the study.
sd_low_crab: the standard deviation of the soil characteristic measured in the low crab treatment within the study.
n_low_crab: the sample size of the soil characteristic measured in the low crab treatment within the study.
mean_high_crab: the mean value of the soil characteristic measured in the high crab treatment within the study.
sd_high_crab: the standard deviation of the soil characteristic measured in the high crab treatment within the study.
n_high_crab: the sample size of the soil characteristic measured in the high crab treatment within the study.
pooled_sd: the pooled standard deviation of the high and low crab treatments for each study.
crab_density: categorical variable noting if the study documented relative burrowing crab density within their study using burrow density (burrow) or counts of individuals (individuals).
hedges_d: the hedges d effect size calculated for the effects of burrowing crabs on the measured sediment characteristic. Hedges d values were calculated in OpenMee software (see code/software below). Positive effect sizes indicate that burrowing crabs increased the value of the sediment measurement, while negative effect sized indicate that burrowing crabs decreased the value of the sediment measurement.
hedges_d_var: the variation of the hedges d effect size calculated for the effects of burrowing crabs on the measured sediment characteristic. Hedges d variation values were calculated in OpenMee software (see code/software below).

Missing data codes: na

Sharing/Access information

All data are included in the provided datafiles.

Code/Software

Hedges’ d (hereafter, d) effect sizes were calculated using meta-analysis using OpenMEE software (Build date: 26 July 2016; Wallace et al. 2017).

Wallace, B. C., M. J. Lajeunesse, G. Dietz, I. J. Dahabreh, T. A. Trikalinos, C. H. Schmid, and J. Gurevitch. 2017. OpenMEE: Intuitive, open-source software for meta-analysis in ecology and evolutionary biology. Methods in Ecology and Evolution 8:941–947.

Search string development and literature survey.

To develop our search string, we consulted the preferred reporting items for systematic reviews and meta-analyses (PRISMA; Moher et al. 2009, Page et al. 2021) and implemented a modified version of the Population, Intervention, Comparison, Outcome (PICO) approach (Foster and Jewell 2017). We defined our populations as burrowing crab communities located within soft-sediment tidal ecosystems. Our variable was broadly defined and included all known pathways by which burrowing crab communities may influence sediments and their functions (e.g., bioturbation, excavation, burrowing, particle reworking, herbivory, facilitation). The outcome was any change in edaphic conditions or sediment functions. The final search string is as follows (the string is presented in sections to specify the intent of each group of search terms, underlined headings were not included in the Boolean string):

Crab Engineer Populations: ((burrowing NEAR/0 crab) OR crab OR (ecosystem NEAR/0 engineer)) OR (uca OR leptuca OR minuca OR (fiddler NEAR/0 crab) OR ocypodid) OR (sesarm OR grapsid OR purple marsh crab) OR (neohelice OR chasmagnathus) OR (pachygrapsus OR ("lined shore" NEAR/0 crab))

AND

Crab Engineer Effect Pathways: ((bioturbation OR bio-irrigation OR bioengineering OR excavation OR burrow OR biomixing OR (particle NEAR/0 rework) OR ventiliat OR morphodynamic OR geomorphic) OR (sediment OR soil OR (intertidal NEAR/0 sediment*)) OR (herbivory OR mutualism OR "top-down control" OR (ecosystem NEAR/0 engineer) OR consum OR graz OR facilitat))

AND

Crab Engineering Outcomes for Sediments: (carbon OR "organic matter" OR decompos OR decay OR respira OR efflux OR (methane OR (CH4)) OR ("carbon dioxide" OR (CO2)) OR fixation OR carbon NEAR/0 flux) OR (nitrogen OR denitrification OR nitrification OR anammox OR DNRA OR nitrate OR ammonium OR nitrite) OR ((sediment NEAR/0 biogeochemistry) OR biogeochemistry OR (sediment NEAR/0 chemistry) OR (soil NEAR/0 chemistry) OR redox OR reduction OR oxygenation OR oxidation OR iron OR sulfur OR sulfate OR manganese) OR (erosion OR erod* OR sediment* OR accret* OR deposit* OR accumulat* OR import* OR export*) OR (nutrient cycling OR nutrient*)

AND

Focal Burrowing Crab Habitats: ((salt NEAR/0 marsh) OR saltmarsh OR marsh OR (salt NEAR/0 panne) OR Spartina OR Juncus OR Phragmities OR Salicornia OR Sarcocornia) OR (mangrove OR (mangrove NEAR/0 tree) OR Avicennia OR Rhizphora) OR (mudflat OR (mud NEAR/0 flat)) OR (tidal OR coastal)

NOT

Exclude: (dune OR freshwater) OR (metal OR pesticide OR pollut) OR (larva OR embryo) OR (seagrass OR eelgrass).

We input our Boolean search string into Web of Science (WoS) Core Collection (http://isiknowledge.com/) on 03 September 2021 and restricted the search to journal articles only. This search yielded 1424 articles. To capture as much of the literature as possible, we also input our Boolean search string into the WoS BIOSIS Previews, WoS Biological Abstracts, and Zoological Record databases on 03 September 2021. The four database searches were merged, and duplicates removed using Endnote (https://endnote.com/). This yielded a merged RIS file containing 1424 unique articles.

Literature screening.

We input our merged RIS files into Rayyan (https://rayyan.ai/; Ouzzani et al. 2016). In Rayyan, each article (n = 1424) was randomly allocated to two blind reviewers. Reviewers evaluated the title and abstract of each article to determine if it should be included, excluded, or reconsidered (i.e., “maybe” in Rayyan software). Included articles needed to evaluate the relationship between burrowing crab density (relative or absolute) on edaphic conditions and sediment functions in a soft-sediment tidal ecosystem. Articles were excluded if they did not include burrowing crabs, quantify sediment properties and functions, or perform the study in a soft-sediment tidal habitat. We also excluded articles that were 1) qualitative with no primary data, 2) modeling or meta-analyses with no primary data, or 3) a graduate thesis where the data was also in a published article. Reviewers could also mark the article for reconsideration if they felt the title and abstract did not provide enough information to include or exclude the article.

Our first review of articles yielded 102 included articles, 112 ‘maybe’ articles, and 1210 excluded articles. We did a secondary review of all included and ‘maybe’ articles (n = 214). This secondary review involved a single reviewer reading the article in its entirety and determining if the article was eligible for inclusion based on the same criteria used during the first review in Rayyan. Our second review resulted in 87 articles that we considered for data collection. After reviewing these 87 articles, we decided to focus on articles that used comparative methodologies to assess edaphic conditions and sediment functions in habitats with high vs. low relative burrowing crab density. We chose to focus on articles that used comparative approaches, rather than articles that took a strictly correlative approach, because studies used a variety of burrowing crab density proxies (e.g., individual crab vs. burrow counts) and standardizing measurements of edaphic conditions and sediment functions across studies limited our sample sizes. Ultimately, we had 56 articles that we used for data collection. We also added three additional articles (Walker et al. 2021, Rinehart et al. 2023, Rinehart et al. in prep) that were close to publication at the time of the search. This resulted in our data set containing 59 total articles.

Data collection.

From each article, we collected data on sediment physical conditions, nutrient stocks, and ecosystem functions in habitats with relatively high vs. relatively low burrowing crab activity. We extracted data from tables, text, and figures (using Web Plot Digitizer; Rohatgi 2022). For each relevant study, we extracted the sample size, mean, and variance (standard error or standard deviation). Because the mean was not reported for all data in five articles (Martinetto et al. 2011, Escapa et al. 2015, Alvarez et al. 2018, Giorgini et al. 2019, Wang et al. 2020), we extracted the sample size, minimum, first quartile, median, third quartile, and maximum values of sediment characteristics and functions for these studies. We used this information to estimate the means and standard deviations for these studies (n = 50; Wan et al. 2014). If articles included multiple relevant independent studies, we extracted each individual study. This process resulted in 1422 total studies evaluating the relative effect of burrowing crabs on coastal soft-sediments and their functions. For each extracted study, we also recorded the following potential covariates: (1) ecosystem type (categorical: tidal flats, tidal marsh, mangrove forest), (2) Crab burrow density (continuous: density per m²), (3) vegetation (categorical: vegetated, unvegetated), (4) burrowing crab superfamily (categorical: Grapsoidea, Ocypodoidea, mixed community), and (5) methodology (categorical: manipulative, observational).

Effect size calculations.

We conducted our meta-analysis using OpenMEE software (Build date: 26 July 2016; Wallace et al. 2017). We calculated the Hedges’ d (hereafter, d) to evaluate the effects of burrowing crabs (present/absent) on coastal sediment characteristics and functions (Hedges 1981). The Hedges’ d represents the relative difference between ‘Crab Present’ treatments and ‘Crab Absent’ treatments divided by the pooled standard deviation (Hedges 1981). If manuscripts included multiple ‘Crab Present’ treatments (e.g., Moore 2019), an individual Hedges’ d calculation was performed for each ‘Crab Present’ treatment relative to the ‘Crab Absent’ treatment. We used d because it is less sensitive to small sample sizes than other effect size calculations (Osenberg et al. 1997, Lajeunesse and Forbes 2003). A positive effect size indicates that burrowing crabs increased the response variable, while a negative effect size indicates that burrowing crabs decreased the response variable.

Variability and publication bias

We tested for potential publication bias by calculating Kendall’s Rank Correlations (T_b) between effect size and pooled variance within each dataset (Begg and Mazumdar 1994).

References

Alvarez, M. F., M. C. Bazterrica, E. Fanjul, M. S. Addino, M. S. Valiñas, O. O. Iribarne, and F. Botto. 2018. Effects of two estuarine intertidal polychaetes on infaunal assemblages and organic matter under contrasting crab bioturbation activity. Journal of Sea Research 139:33–40.

Begg, C. B., and M. Mazumdar. 1994. Operating Characteristics of a Rank Correlation Test for Publication Bias. Biometrics 50:1088–1101.

Escapa, M., G. M. E. Perillo, and O. Iribarne. 2015. Biogeomorphically driven salt pan formation in Sarcocornia-dominated salt-marshes. Geomorphology 228:147–157.

Foster, M. J., and S. T. Jewell. 2017. Assembling the pieces of a systematic review: A guide for librarians. Page (M. J. Foster and S. T. Jewell, Eds.). Rowman & Littlefield Publishers, Washington, DC.

Giorgini, M., A. Miguez, K. S. Esquius, C. D. De Astarloa, O. Iribarne, E. Fanjul, and M. Escapa. 2019. Regenerative bioturbation by intertidal burrowing crabs modifies microphytobenthic composition and enhances primary production in SW Atlantic mudflats. Marine Ecology Progress Series 632:43–57.

Hedges, L. V. 1981. Distribution Theory for Glass ’ s Estimator of Effect Size and Related Estimators. Journal of Educational Statistics 6:107–128.

Lajeunesse, M. J., and M. R. Forbes. 2003. Variable reporting and quantitative reviews: A comparison of three meta-analytical techniques. Ecology Letters 6:448–454.

Martinetto, P., G. Palomo, M. Bruschetti, and O. Iribarne. 2011. Similar effects on sediment structure and infaunal community of two competitive intertidal soft-bottom burrowing crab species. Journal of the Marine Biological Association of the United Kingdom 91:1385–1393.

Moher, D., A. Liberati, J. Tetzlaff, and D. G. Altman. 2009. Academia and Clinic Annals of Internal Medicine Preferred Reporting Items for Systematic Reviews and Meta-Analyses : Annals of Internal Medicine 151:264–269.

Moore, A. 2019. What is the role of ecosystem engineers in New England salt marshes? A mesocosm study of the fiddler crab and the purple marsh crab. Wetlands 39:371-379.

Osenberg, C. W., O. Sarnelle, and S. D. Cooper. 1997. Effect size in ecological experiments: The application of biological models in meta-analysis. American Naturalist 150:798–812.

Ouzzani, M., H. Hammady, Z. Fedorowicz, and A. Elmagarmid. 2016. Rayyan-a web and mobile app for systematic reviews. Systematic Reviews 5:210.

Page, M. J., J. E. McKenzie, P. M. Bossuyt, I. Boutron, T. C. Hoffmann, C. D. Mulrow, L. Shamseer, J. M. Tetzlaff, E. A. Akl, S. E. Brennan, R. Chou, J. Glanville, J. M. Grimshaw, A. Hróbjartsson, M. M. Lalu, T. Li, E. W. Loder, E. Mayo-Wilson, S. McDonald, L. A. McGuinness, L. A. Stewart, J. Thomas, A. C. Tricco, V. A. Welch, P. Whiting, and D. Moher. 2021. The PRISMA 2020 statement: An updated guideline for reporting systematic reviews. BMJ 372:n71.

Rinehart, S., J. M. Dybiec, B. Mortazavi, and J. A. Cherry. 2023. Stratified vertical sediment profiles increase burrowing crab effects on salt marsh edaphic conditions. Ecosphere 14:e4431.

Rinehart, S., and D. Hawlena. 2020. The effects of predation risk on prey stoichiometry: a meta-analysis. Ecology 101:e3037.

Rohatgi, A. 2022. WebPlotDigitizer. Pacifica, California.

Walker, J. B., S. A. Rinehart, W. K. White, E. D. Grosholz, and J. D. Long. 2021. Local and regional variation in effects of burrowing crabs on plant community structure. Ecology 102:e03244.

Wan, X., W. Wang, J. Liu, and T. Tong. 2014. Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range. BMC Medical Research Methodology 14:1–13.

Wang, X., Y. Li, B. Guan, J. Yu, Z. Zhang, H. Wu, and K. Zhang. 2020. Beneficial effects of crab burrowing on the surface soil properties of newly formed mudflats in the Yellow River Delta. Ecohydrology and Hydrobiology 20:548–555.