Published May 24, 2024
| Version v1
Dataset
Open
Peatland Decomposition Database (1.0.0)
Description
1 Introduction
The Peatland Decomposition Database (PDD) stores data from published litterbag experiments related to peatlands. Currently, the database focuses on northern peatlands and Sphagnum litter and peat, but it also contains data from some vascular plant litterbag experiments. Currently, the database contains entries from 33 studies, 2,156 litterbag experiments, and 7,253 individual samples with 117,493 measurements for various attributes (e.g. relative mass remaining, N content, holocellulose content, mesh size). The aim is to provide a harmonized data source that can be useful to re-analyse existing data and to plan future litterbag experiments.
The Peatland Productivity and Decomposition Parameter Database (PPDPD) (Bona et al. 2018) is similar to the Peatland Decomposition Database (PDD) in that both contain data from peatland litterbag experiments. The differences are that both databases partly contain different data, that PPDPD additionally contains information on vegetation productivity, which PDD does not, and that PDD provides more information and metadata on litterbag experiments, and also measurement errors.
2 Methods
2.1 Data collection
Data for the database was collected from published litterbag studies, by extracting published data from figures, tables, or other data sources, and by contacting the authors of the studies to obtain raw data. All data processing was done with R (R version 4.2.0 (2022-04-22)) (R Core Team 2022).
Studies were identified via a Scopus search with search string (TITLE-ABS-KEY ( peat* AND ( "litter bag" OR "decomposition rate" OR "decay rate" OR "mass loss")) AND NOT ("tropic*")) (2022-12-17). These studies were further screened to exclude those which do not contain litterbag data or which recycle data from other studies that have already been considered. Additional studies with litterbag experiments in northern peatlands we were aware of, but which were not identified in the literature search were added to the list of publications. For studies not older than 10 years, authors were contacted to obtain raw data, however this was successful only in few cases. To date, the database focuses on Sphagnum litterbag experiments and there are still studies that were identified by the literature search and for which data have not been included yet in the database.
Data from figures were extracted using the package ‘metaDigitise’ (1.0.1) (Pick, Nakagawa, and Noble 2018). Data from tables were extracted manually.
Data from the following studies are currently included: Farrish and Grigal (1985), Bartsch and Moore (1985), Farrish and Grigal (1988), Vitt (1990), Hogg, Lieffers, and Wein (1992), Sanger, Billett, and Cresser (1994), Hiroki and Watanabe (1996), Szumigalski and Bayley (1996), Prevost, Belleau, and Plamondon (1997), Arp, Cooper, and Stednick (1999), Robbert A. Scheffer and Aerts (2000), R. A. Scheffer, Van Logtestijn, and Verhoeven (2001), Limpens and Berendse (2003), Waddington, Rochefort, and Campeau (2003), Asada, Warner, and Banner (2004), Thormann, Bayley, and Currah (2001), Asada and Warner (2005), Trinder, Johnson, and Artz (2008), Breeuwer et al. (2008), Trinder, Johnson, and Artz (2009), Bragazza and Iacumin (2009), Hoorens, Stroetenga, and Aerts (2010), Straková et al. (2010), Straková et al. (2012), Orwin and Ostle (2012), Lieffers (1988), Manninen et al. (2016), Johnson and Damman (1991), Bengtsson, Rydin, and Hájek (2018a), Bengtsson, Rydin, and Hájek (2018b), Bengtsson, Granath, and Rydin (2017), Bengtsson, Granath, and Rydin (2016), Hagemann and Moroni (2015), Hagemann and Moroni (2016), B. Piatkowski et al. (2021), B. T. Piatkowski et al. (2021), Mäkilä et al. (2018), Golovatskaya and Nikonova (2017)
3 Database records
The database is a ‘MariaDB’ database and the database schema was designed to store data and metadata following the Ecological Metadata Language (EML) (Jones et al. 2019). Descriptions of the tables are shown in Tab. 1
The database contains general metadata relevant for litterbag experiments (e.g., geographical, temporal, and taxonomic coverage, mesh sizes, experimental design). However, it does not contain a detailed description of sample handling, sample preprocessing methods, site descriptions, because there currently are no discipline-specific metadata and reporting standards.
Table 1: Description of the individual tables in the database.| Name | Description |
|---|---|
| attributes | Defines the attributes of the database and the values in column attribute_name in table data. |
| citations | Stores bibtex entries for references and data sources. |
| citations_to_datasets | Links entries in table citations with entries in table datasets. |
| custom_units | Stores custom units. |
| data | Stores measured values for samples, for example remaining masses. |
| datasets | Lists the individual datasets. |
| experimental_design_format | Stores information on the experimental design of litterbag experiments. |
| measurement_scales, measurement_scales_date_time, measurement_scales_interval, measurement_scales_nominal, measurement_scales_ordinal, measurement_scales_ratio | Defines data value types. |
| missing_value_codes | Defines how missing values are encoded. |
| samples | Stores information on individual samples. |
| samples_to_samples | Links samples to other samples, for example litter samples collected in the field to litter samples collected during the incubation of the litterbags. |
| units, unit_types | Stores information on measurement units. |
4 Attributes
Table 2: Definition of attributes in the Peatland Decomposition Database and entries in the columnattribute_name in table data.
| Name | Definition | Example value | Unit | Measurement scale | Number type | Minimum value | Maximum value | String format |
|---|---|---|---|---|---|---|---|---|
| 4_hydroxyacetophenone_mass_absolute | A numeric value representing the content of 4-hydroxyacetophenone, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| 4_hydroxyacetophenone_mass_relative_mass | A numeric value representing the content of 4-hydroxyacetophenone, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| 4_hydroxybenzaldehyde_mass_absolute | A numeric value representing the content of 4-hydroxybenzaldehyde, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| 4_hydroxybenzaldehyde_mass_relative_mass | A numeric value representing the content of 4-hydroxybenzaldehyde, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| 4_hydroxybenzoic_acid_mass_absolute | A numeric value representing the content of 4-hydroxybenzoic acid, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| 4_hydroxybenzoic_acid_mass_relative_mass | A numeric value representing the content of 4-hydroxybenzoic acid, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| abbreviation | In table custom_units: A string representing an abbreviation for the custom unit. |
gC | NA | nominal | NA | NA | NA | NA |
| acetone_extractives_mass_absolute | A numeric value representing the content of acetone extractives, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| acetone_extractives_mass_relative_mass | A numeric value representing the content of acetone extractives, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| acetosyringone_mass_absolute | A numeric value representing the content of acetosyringone, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| acetosyringone_mass_relative_mass | A numeric value representing the content of acetosyringone, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| acetovanillone_mass_absolute | A numeric value representing the content of acetovanillone, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| acetovanillone_mass_relative_mass | A numeric value representing the content of acetovanillone, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| arabinose_mass_absolute | A numeric value representing the content of arabinose, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| arabinose_mass_relative_mass | A numeric value representing the content of arabinose, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| ash_mass_absolute | A numeric value representing the content of ash (after burning at 550°C). | 4 | g | ratio | real | 0 | Inf | NA |
| ash_mass_relative_mass | A numeric value representing the content of ash (after burning at 550°C). | 0.05 | g/g | ratio | real | 0 | Inf | NA |
| attribute_definition | A free text field with a textual description of the meaning of attributes in the dpeatdecomposition database. | NA | NA | nominal | NA | NA | NA | NA |
| attribute_name | A string describing the names of the attributes in all tables of the dpeatdecomposition database. | attribute_name | NA | nominal | NA | NA | NA | NA |
| bibtex | A string representing the bibtex code used for a literature reference throughout the dpeatdecomposition database. | Galka.2021 | NA | nominal | NA | NA | NA | NA |
| bounds_maximum | A numeric value representing the minimum possible value for a numeric attribute. | 0 | NA | interval | real | Inf | Inf | NA |
| bounds_minimum | A numeric value representing the maximum possible value for a numeric attribute. | INF | NA | interval | real | Inf | Inf | NA |
| bulk_density | A numeric value representing the bulk density of the sample [g cm-3]. | 0,2 | g/cm^3 | ratio | real | 0 | Inf | NA |
| C_absolute | The absolute mass of C in the sample. | 1 | g | ratio | real | 0 | Inf | NA |
| C_relative_mass | The absolute mass of C in the sample. | 1 | g/g | ratio | real | 0 | Inf | NA |
| C_to_N | A numeric value representing the C to N ratio of the sample. | 35 | g/g | ratio | real | 0 | Inf | NA |
| C_to_P | A numeric value representing the C to P ratio of the sample. | 35 | g/g | ratio | real | 0 | Inf | NA |
| Ca_absolute | The absolute mass of Ca in the sample. | 1 | g | ratio | real | 0 | Inf | NA |
| Ca_relative_mass | The absolute mass of Ca in the sample. | 1 | g/g | ratio | real | 0 | Inf | NA |
| cation_exchange_capacity_absolute | A numeric value representing the cation exchange capacity. | 10 | mol | ratio | real | 0 | Inf | NA |
| cation_exchange_capacity_relative_mass | A numeric value representing the cation exchange capacity relative to sample mass. | 200 | mol/g | ratio | real | 0 | Inf | NA |
| cellulose_mass_absolute | A numeric value representing the content of cellulose, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| cellulose_mass_relative_mass | A numeric value representing the content of cellulose, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| comments_measurement | A string representing comments on a measurement. | NA | NA | nominal | NA | NA | NA | NA |
| comments_samples | A free text field where you can enter all information related to the sample that is not covered by the remaining fields. For example you could provide information on potential contamination sources, issues with specific parameters, additional information to the sampling site, e.g. present vegetation, past vegetation, specific conditions during sampling, … . | … | NA | nominal | NA | NA | NA | NA |
| description | A free text field. In table “custom_units”: A description of a custom unit. | NA | NA | nominal | NA | NA | NA | NA |
| dichloromethane_extractives_mass_absolute | A numeric value representing the content of dichlromethane extractives, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| dichloromethane_extractives_mass_relative_mass | A numeric value representing the content of dichlromethane extractives, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| dimension | A string representing the dimension of the unit. | L | NA | nominal | NA | NA | NA | NA |
| error | A numeric value representing the error of the measured value. The unit of the error is defined by the corresponding attribute_name. |
1.2 | NA | ratio | real | 0 | Inf | NA |
| error_type | A character representing the type of the error of a measured value (e.g., sd, 95% interval, etc.). | sd | NA | nominal | NA | NA | NA | NA |
| ethanol_extractives_mass_absolute | A numeric value representing the content of ethanol extractives, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| ethanol_extractives_mass_relative_mass | A numeric value representing the content of ethanol extractives, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| experimental_design | A character of the format ‘x_y_z_…’, where x, y, z, …, are integers differentiating hierarchical groups of an experimental design. These groups are explained in table experimental_design_format. |
1_3_1 | NA | nominal | NA | NA | NA | NA |
| experimental_design_format | A string decoding the experimental design encoded in experimental_design. |
site_area in site_plot | NA | nominal | NA | NA | NA | NA |
| explanation | In table missing_value_codes: A string explaining what the corresponding missing value code means. |
… | NA | nominal | NA | NA | NA | NA |
| Fe_absolute | The absolute mass of Fe in the sample. | 1 | g | ratio | real | 0 | Inf | NA |
| Fe_relative_mass | The absolute mass of Fe in the sample. | 1 | g/g | ratio | real | 0 | Inf | NA |
| ferulic_acid_mass_absolute | A numeric value representing the content of ferulic acid, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| ferulic_acid_mass_relative_mass | A numeric value representing the content of ferulic acid, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| file | A string representing a path to a file. For table experimental_design_format: Path to a csv file providing details on the experimental design and manipulations. |
NA | NA | nominal | NA | NA | NA | NA |
| format_string | A string defining the format of a nominal variable. | YYYY-MM-DD | NA | nominal | NA | NA | NA | NA |
| galactose_mass_absolute | A numeric value representing the content of galactose, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| galactose_mass_relative_mass | A numeric value representing the content of galactose, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| galacturonic_acid_mass_absolute | A numeric value representing the content of galacturonic acid, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| galacturonic_acid_mass_relative_mass | A numeric value representing the content of galacturonic acid, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| glucose_mass_absolute | A numeric value representing the content of glucose, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| glucose_mass_relative_mass | A numeric value representing the content of glucose, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| glucuronic_acid_mass_absolute | A numeric value representing the content of glucuronic acid, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| glucuronic_acid_mass_relative_mass | A numeric value representing the content of glucuronic acid, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| ground_slope | The slope of the sample (land surface) as fraction of the vertical distance covered and the horizontal distance. | 0.2 | cm/cm | ratio | real | 0 | Inf | NA |
| holocellulose_mass_absolute | A numeric value representing the absolute holocellulose mass in the sample. | 0.45 | g | ratio | real | 0 | Inf | NA |
| holocellulose_mass_relative_mass | A numeric value representing the holocellulose content of the sample [g/g]. | 0.45 | g/g | ratio | real | 0 | 1 | NA |
| id_citation | An integer value representing an id for each entry in the table “citations“ in the dpeatdecomposition database. | 1 | NA | interval | natural | 1 | Inf | NA |
| id_dataset | A numeric id for the dataset (starting with 1 and increasing by 1; for one data contribution, this should be 1 for all samples and the appropriate id is assigned when the data are merged into the database). | 1 | NA | interval | natural | 1 | Inf | NA |
| id_measurement | A numeric id for measurements (starting with 1 and increasing by 1). This means that each measurement gets its own rows and measurements for different attributes are considered independent, i.e. multiple measurement ids for the same sample just count replicate measurements for any attribute. For attributes with less measurements than for a different attribute, just fill measurements starting from smaller id_measurement and leave the cells in the remaining rows empty. | 1 | NA | interval | natural | 1 | Inf | NA |
| id_measurement_denominator | An integer value representing the identifier for the measurement which is used as denominator in computing a relative quantity (e.g. the absolute mass of the initial sample when computing the mass fraction relative to the initial sample). | 1 | NA | interval | natural | 1 | Inf | NA |
| id_measurement_numerator | An integer value representing the identifier for the measurement which is used as numerator in computing a relative quantity (e.g. the absolute mass of the sample when computing the mass fraction relative to the initial sample). | 1 | NA | interval | natural | 1 | Inf | NA |
| id_measurement_scale | An integer value representing an id for each entry in the table “measurement_scales“ in the dpeatdecomposition database. | 1 | NA | interval | natural | 1 | Inf | NA |
| id_missing_value_code | An integer value representing an id for each entry in the table “missing_value_codes“ in the dpeatdecomposition database. | 1 | NA | interval | natural | 1 | Inf | NA |
| id_sample | A numeric id for the sample (starting with 1 and increasing by 1). | 1 | NA | interval | natural | 1 | Inf | NA |
| id_sample_child | An integer representing an identifier for the child (resulting) sample of the transition (some change to a sample). | 1 | NA | interval | natural | 1 | Inf | NA |
| id_sample_incubation_start | An integer representing an identifier for the sample which is the sample at the start of the incubation (incubation_duration == 0). |
1 | NA | interval | natural | 1 | Inf | NA |
| id_sample_origin | An integer representing an identifier for the sample which is the original sample in a line of transitions of a sample (modifications of a sample). | 1 | NA | interval | natural | 1 | Inf | NA |
| id_sample_parent | An integer representing an identifier for the parent (initial) sample of the transition (some change to a sample). | 1 | NA | interval | natural | 1 | Inf | NA |
| id_unit | An integer value representing an id for each entry in the table “units“ in the dpeatdecomposition database. | 1 | NA | interval | natural | 1 | Inf | NA |
| incubation_duration | A numeric value representing the number of days over which a sample was incubated. | 45 | d | ratio | real | 0 | Inf | NA |
| incubation_environment | A character defining the environment in which a litterbag sample was incubated (e.g. ‘peat’, ‘container’, …). | peat | NA | nominal | NA | NA | NA | NA |
| is_incubated | A logical value indicating whether a sample was collected during the decomposition incubation of a litterbag experiment or not. | TRUE | NA | nominal | NA | NA | NA | NA |
| K_absolute | The absolute mass of K in the sample. | 1 | g | ratio | real | 0 | Inf | NA |
| K_relative_mass | The absolute mass of K in the sample. | 1 | g/g | ratio | real | 0 | Inf | NA |
| Klason_lignin_mass_absolute | A numeric value representing the absolute Klason lignin mass in the sample. | 0.26 | g | ratio | real | 0 | Inf | NA |
| Klason_lignin_mass_relative_mass | A numeric value representing the Klason lignin content of the sample [g/g]. | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| mannose_mass_absolute | A numeric value representing the content of mannose, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| mannose_mass_relative_mass | A numeric value representing the content of mannose, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| mass_absolute | The mass of the sample. | 1200 | mg | ratio | real | 0 | Inf | NA |
| mass_relative_mass | The mass of the sample divided by the mass of a sample (e.g. the sample before decomposition). | 0.87 | g/g | ratio | real | 0 | Inf | NA |
| measurement_scale | A string representing the measurement scale for a value. | nominal | NA | nominal | NA | NA | NA | NA |
| mesh_size_absolute | The width of the mesh the litterbags are made of. | 0.2 | um | ratio | real | 0 | Inf | NA |
| Mg_absolute | The absolute mass of Mg in the sample. | 1 | g | ratio | real | 0 | Inf | NA |
| Mg_relative_mass | The absolute mass of Mg in the sample. | 1 | g/g | ratio | real | 0 | Inf | NA |
| Mn_absolute | The absolute mass of Mn in the sample. | 1 | g | ratio | real | 0 | Inf | NA |
| Mn_relative_mass | The absolute mass of Mn in the sample. | 1 | g/g | ratio | real | 0 | Inf | NA |
| multiplier_to_si | A numeric value representing the value with which a given value with a certain measurement unit has to be multiplied in order to convert it to a related SI unit. | 100 | dimensionless | interval | real | Inf | Inf | NA |
| N_absolute | The absolute mass of nitrogen in the sample. | 1.2 | mg | ratio | real | 0 | Inf | NA |
| N_relative_mass | The mass of the nitrogen in the sample divided by the mass of a sample (e.g. the sample before decomposition). | 0.013 | g/g | ratio | real | 0 | Inf | NA |
| number_type | A string representing the number type of a numeric variable. | NA | NA | nominal | NA | NA | NA | NA |
| P_absolute | The absolute mass of P in the sample. | 1 | g | ratio | real | 0 | Inf | NA |
| p_coumaric_acid_mass_absolute | A numeric value representing the content of p-coumaric acid, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| p_coumaric_acid_mass_relative_mass | A numeric value representing the content of p-coumaric acid, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| P_relative_mass | The absolute mass of P in the sample. | 1 | g/g | ratio | real | 0 | Inf | NA |
| parent_si | A string representing the SI unit from which a certain derived unit is derived. | m | NA | nominal | NA | NA | NA | NA |
| pH | A numeric value representing the pH value of the sample. | 5,4 | dimensionless | interval | real | Inf | Inf | NA |
| phenolics_PHBA_equivalents_mass_absolute | A numeric value representing the mass content of phenolics (p-hydroxy benzoic acid equivalent). | 10 | g | ratio | real | 0 | Inf | NA |
| phenolics_PHBA_equivalents_mass_relative_mass | A numeric value representing the mass content of phenolics (p-hydroxy benzoic acid equivalent). | 0.04 | g/g | ratio | real | 0 | 1 | NA |
| phenolics_tannic_acid_equivalents_mass_absolute | A numeric value representing the mass content of phenolics (tannic acid equivalent). | 10 | g | ratio | real | 0 | Inf | NA |
| phenolics_tannic_acid_equivalents_mass_relative_mass | A numeric value representing the mass content of phenolics (tannic acid equivalent). | 0.04 | g/g | ratio | real | 0 | 1 | NA |
| power | An integer value. The power to which the dimension is raised. | 2 | dimensionless | interval | integer | Inf | Inf | NA |
| rhamnose_mass_absolute | A numeric value representing the content of rhamnose, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| rhamnose_mass_relative_mass | A numeric value representing the content of rhamnose, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| root_diameter_absolute | The diameter of roots in the sample. | 2 | mm | ratio | real | 0 | Inf | NA |
| S_absolute | The absolute mass of S in the sample. | 1 | g | ratio | real | 0 | Inf | NA |
| S_relative_mass | The absolute mass of S in the sample. | 1 | g/g | ratio | real | 0 | Inf | NA |
| sample_depth_lower | A numeric value representing the depth of the lower boundary of a sample relative to the land surface (e.g. peat surface) [cm]. | 15 | cm | interval | real | Inf | Inf | NA |
| sample_depth_upper | A numeric value representing the depth of the upper boundary of a sample relative to the land surface (e.g. peat surface) [cm]. | 12 | cm | interval | real | Inf | Inf | NA |
| sample_label | A string representing a label for each sample. | S1 | NA | nominal | NA | NA | NA | NA |
| sample_microhabitat | A string describing the microhabitat where the sample was collected. For peat, this should be one of ‘hummock’, ‘hollow’, ‘lawn’, ‘pond’. In other cases, a custom value can be used. | hummock | NA | nominal | NA | NA | NA | NA |
| sample_size | An integer representing the number of individual measurements which were used to compute the value in column value. |
1 | NA | interval | natural | 1 | Inf | NA |
| sample_treatment | A string with an description of an experimental tratment if this was applied. By default, this should be ‘control’, indicating that there was no manipulation. If there was any experimental manipulation, this can be abbreviated by a label (e.g. by a treatment level) that is defined in the textual description of the project (in the file ‘description.docx’). | control | NA | nominal | NA | NA | NA | NA |
| sample_type | A string describing the type of the sample. Must be one of ‘peat’, ‘dom’, ‘vegetation’, ‘litter’. | peat | NA | nominal | NA | NA | NA | NA |
| sample_type2 | A string describing the type of the sample. Here you can provide individual (own) categories which may provide more details than the column sample_type. | shoots | NA | nominal | NA | NA | NA | NA |
| sample_wet_mass_absolute | A numeric value representing the mass of the wet sample [g]. | 5.6 | g | ratio | real | 0 | Inf | NA |
| sampling_altitude | A numeric value representing the altitude of the exact sampling position [m above sea level]. | 543 | m | ratio | real | Inf | Inf | NA |
| sampling_day | An integer representing the day in which a sample was collected. | 1 | NA | interval | natural | 1 | 31 | NA |
| sampling_latitude | A numeric value representing the latitude coordinates of the exact sampling position (in the EPSG:3857 projection coordinate system — this is the system used by Google and is based on the WGS 84 reference system) [°N]. | 40447 | NA | interval | real | -180 | 180 | NA |
| sampling_longitude | A numeric value representing the longitude coordinates of the exact sampling position (in the EPSG:3857 projection coordinate system — this is the system used by Google and is based on the WGS 84 reference system) [°W]. | 79983 | NA | interval | real | -180 | 180 | NA |
| sampling_month | An integer representing the month in which a sample was collected. | 1 | NA | interval | natural | 1 | 12 | NA |
| sampling_year | An integer representing the year in which a sample was collected. | 1 | NA | interval | natural | 1 | Inf | NA |
| site_name | A character representing the name of the site where the sample was collected. | Mer Bleue | NA | nominal | NA | NA | NA | NA |
| soluble_Klason_lignin_mass_absolute | A numeric value representing the mass content of soluble Klason lignin (following Ehrman 1996). | 10 | g | ratio | real | 0 | Inf | NA |
| soluble_Klason_lignin_mass_relative_mass | A numeric value representing the mass content of soluble Klason lignin (following Ehrman 1996). | 0.04 | g/g | ratio | real | 0 | 1 | NA |
| soluble_lignin_mass_absolute | A numeric value representing the content of soluble lignin, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| soluble_lignin_mass_relative_mass | A numeric value representing the content of soluble lignin, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| sphagnan_mass_absolute | A numeric value representing the mass content of sphagnan (Ballance et al., 2007). | 10 | g | ratio | real | 0 | Inf | NA |
| sphagnan_mass_relative_mass | A numeric value representing the mass content of sphagnan (Ballance et al., 2007). | 0.04 | g/g | ratio | real | 0 | 1 | NA |
| standard_unit | A logical value indicating if the unit is a standard unit of the Ecological Metadata Language or not. | TRUE | NA | nominal | NA | NA | NA | NA |
| syringe_aldehyde_mass_absolute | A numeric value representing the content of syringe aldehyde, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| syringe_aldehyde_mass_relative_mass | A numeric value representing the content of syringe aldehyde, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| syringic_acid_mass_absolute | A numeric value representing the content of syringic acid, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| syringic_acid_mass_relative_mass | A numeric value representing the content of syringic acid, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| taxon_organ | A string describing the organ of a taxon the sample represents (if the sample represents a taxon). For example, if the sample is Carex lasiocarpa, this could be ‘shoot’, or ‘root’, or ‘leaves’. | root | NA | nominal | NA | NA | NA | NA |
| taxon_rank_name | A string describing the taxon rank the value in column taxon_rank_value represents (if the sample can be assigned to a specific taxon). For exampe, if the value in column taxon_rank_value is a species name, then you should enter ‘species’ here, or if the value in column taxon_rank_value is a genus name, then you should enter ‘genus’ here. | species | NA | nominal | NA | NA | NA | NA |
| taxon_rank_value | A string describing the taxon rank value of the sample (if the sample can be assigned to a taxon). For example, if the sample is a distinct species, enter the scientific species name here, or if the sample can be assigned to a genus, enter the scientific genus name here. | Sphagnum magellanicum | NA | nominal | NA | NA | NA | NA |
| temperature | A numeric value representing the temperature of the sample [K]. | 293.4 | K | ratio | real | 0 | Inf | NA |
| text_domain_definition | A string representing the text domain for a string. | NA | NA | nominal | NA | NA | NA | NA |
| transition_description | A string representing a description of what happened to a parent sample during its transition to the child sample. | transplantation | NA | nominal | NA | NA | NA | NA |
| udunits_unit | A string representing a measurement unit in the udunits format. | m | NA | nominal | NA | NA | NA | NA |
| unit_type | A string representing the type of a unit. | length | NA | nominal | NA | NA | NA | NA |
| value | A numeric value representing the measured value. The unit of the value is defined by the corresponding attribute_name. |
1.2 | NA | ratio | real | 0 | Inf | NA |
| value_type | A character representing the type of the measured value. One of ‘point’ (for a single measurement without uncertainty), or ‘mean’ (average of multiple measurements). | point | NA | nominal | NA | NA | NA | NA |
| vanillic_acid_mass_absolute | A numeric value representing the content of vanillic acid, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| vanillic_acid_mass_relative_mass | A numeric value representing the content of vanillic acid, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| vanillin_mass_absolute | A numeric value representing the content of vanillin, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| vanillin_mass_relative_mass | A numeric value representing the content of vanillin, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| volume | A numeric value representing the volume of the sample [cm3]. | 20 | cm^3 | ratio | real | 0 | Inf | NA |
| water_extractives_mass_absolute | A numeric value representing the content of water extractives, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| water_extractives_mass_relative_mass | A numeric value representing the content of water extractives, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
| water_mass_absolute | A numeric value representing the water mass content of the sample as mass of water divided by the mass of the wet sample [g] | 5.6 | g | ratio | real | 0 | Inf | NA |
| water_mass_relative_mass | A numeric value representing the water mass content of the sample as mass of water divided by the mass of the wet sample [g/g] | 2.4 | g/g | ratio | real | 0 | 1 | NA |
| water_mass_relative_volume | A numeric value representing the water mass content of the sample as mass of water divided by the volume of the wet sample [g cm-3]. | 0.6 | g/cm^3 | ratio | real | 0 | 1 | NA |
| water_table_depth | A numeric value representing the depth to the water table level relative to the position of the sample. | 23.4 | cm | ratio | real | -Inf | Inf | NA |
| xylose_mass_absolute | A numeric value representing the content of xylose, as described in Straková et al. (2010). | 0.26 | g | ratio | real | 0 | Inf | NA |
| xylose_mass_relative_mass | A numeric value representing the content of xylose, as described in Straková et al. (2010). | 0.26 | g/g | ratio | real | 0 | 1 | NA |
5 Usage notes
5.1 Download
The Peatland Decomposition Database can be downloaded from https://doi.org/10.5281/zenodo.11276065. There you can also download a folder “derived_data” that contains csv files with the experimental design for each study (see attribute file in Tab. 2).
5.2 Set up
The downloaded database needs to be imported in a running MariaDB instance. In a linux terminal, the downloaded sql file can be imported like so:
mysql -u<user> -p<password> dpeatdecomposition < dpeatdecomposition-backup-2024-05-15.sqlHere, <user> and are the respective database user name and password.
5.3 R interface
The R package ‘dpeatdecomposition’ (Teickner and Knorr 2024) provides an R interface to the database, based on the packages ‘RMariaDB’ (Müller et al. 2021), and ‘dm’ (Schieferdecker, Müller, and Bergant 2022).
6 Citation
If you use data from the Peat Decomposition Database, cite the database and each of the original data sources you use. Bibliographic information on each data source are stored in table citations and linked to datasets via table citations_to_datasets.
The database can be cited as: Teickner, Henning and Klaus-Holger Knorr. 2024. “Peatland Decomposition Database (1.0.0).” Zenodo. https://doi.org/10.5281/zenodo.11276065.
Bibtex entries for each dataset can also be obtained using the ‘dpeatdecomposition’ package:
# connect to database
con <-
RMariaDB::dbConnect(
drv = RMariaDB::MariaDB(),
dbname = "dpeatdecomposition",
default.file = "~/my.cnf"
)
# get database as dm object
dm_dpeatdecomposition <-
dpeatdecomposition::dp_get_dm(con, learn_keys = TRUE)
# extract bibtex entries
dm_dpeatdecomposition |>
dm::dm_zoom_to(datasets) |>
dm::left_join(citations_to_datasets, by = "id_dataset") |>
dm::left_join(citations, by = "id_citation") |>
dm::pull_tbl() |>
as.data.frame()
# disconnect
RMariaDB::dbDisconnect(con)A full list of references for the individual datasets is provided in Tab. 3.
Table 3: Sources for each dataset in the Peatland Decomposition Database.| id_dataset | Source |
|---|---|
| 1 | Farrish and Grigal (1985) |
| 2 | Bartsch and Moore (1985) |
| 3 | Farrish and Grigal (1988) |
| 4 | Vitt (1990) |
| 5 | Hogg, Lieffers, and Wein (1992) |
| 6 | Sanger, Billett, and Cresser (1994) |
| 7 | Hiroki and Watanabe (1996) |
| 8 | Szumigalski and Bayley (1996) |
| 9 | Prevost, Belleau, and Plamondon (1997) |
| 10 | Arp, Cooper, and Stednick (1999) |
| 11 | Robbert A. Scheffer and Aerts (2000) |
| 12 | R. A. Scheffer, Van Logtestijn, and Verhoeven (2001) |
| 13 | Limpens and Berendse (2003) |
| 14 | Waddington, Rochefort, and Campeau (2003) |
| 15 | Asada, Warner, and Banner (2004) |
| 16 | Thormann, Bayley, and Currah (2001) |
| 17 | Asada and Warner (2005) |
| 18 | Trinder, Johnson, and Artz (2008) |
| 19 | Breeuwer et al. (2008) |
| 20 | Trinder, Johnson, and Artz (2009) |
| 21 | Bragazza and Iacumin (2009) |
| 22 | Hoorens, Stroetenga, and Aerts (2010) |
| 23 | Straková et al. (2010) |
| 23 | Straková et al. (2012) |
| 24 | Orwin and Ostle (2012) |
| 25 | Lieffers (1988) |
| 26 | Manninen et al. (2016) |
| 27 | Johnson and Damman (1991) |
| 28 | Bengtsson, Rydin, and Hájek (2018a) |
| 28 | Bengtsson, Rydin, and Hájek (2018b) |
| 29 | Bengtsson, Granath, and Rydin (2017) |
| 29 | Bengtsson, Granath, and Rydin (2016) |
| 30 | Hagemann and Moroni (2015) |
| 30 | Hagemann and Moroni (2016) |
| 31 | B. Piatkowski et al. (2021) |
| 31 | B. T. Piatkowski et al. (2021) |
| 32 | Mäkilä et al. (2018) |
| 33 | Golovatskaya and Nikonova (2017) |
7 Acknowledgements
Development of this database was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) grant no. KN 929/23-1 to Klaus-Holger Knorr and grant no. PE 1632/18-1 to Edzer Pebesma.
References
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Asada, Taro, and Barry G. Warner. 2005. “Surface Peat Mass and Carbon Balance in a Hypermaritime Peatland.” Soil Science Society of America Journal 69 (2): 549–62. https://doi.org/10.2136/sssaj2005.0549.
Asada, Taro, Barry G Warner, and Allen Banner. 2004. “Sphagnum Invasion After Clear-Cutting and Excavator Mounding in a Hypermaritime Forest of British Columbia.” Canadian Journal of Forest Research 34 (8): 1730–46. https://doi.org/10.1139/x04-042.
Bartsch, I., and T. R. Moore. 1985. “A Preliminary Investigation of Primary Production and Decomposition in Four Peatlands Near Schefferville, Québec.” Canadian Journal of Botany 63 (7): 1241–48. https://doi.org/10.1139/b85-171.
Bengtsson, Fia, Gustaf Granath, and Håkan Rydin. 2016. “Photosynthesis, Growth, and Decay Traits in Sphagnum – a Multispecies Comparison.” Ecology and Evolution 6 (10): 3325–41. https://doi.org/10.1002/ece3.2119.
———. 2017. “Data from: Photosynthesis, Growth, and Decay Traits in Sphagnum – a Multispecies Comparison.” Dryad. https://doi.org/10.5061/DRYAD.62054.
Bengtsson, Fia, Håkan Rydin, and Tomáš Hájek. 2018a. “Data from: Biochemical Determinants of Litter Quality in 15 Species of Sphagnum.” Dryad. https://doi.org/10.5061/DRYAD.4F8D2.
———. 2018b. “Biochemical Determinants of Litter Quality in 15 Species of Sphagnum.” Plant and Soil 425 (1-2): 161–76. https://doi.org/10.1007/s11104-018-3579-8.
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Bragazza, Luca, and Paola Iacumin. 2009. “Seasonal Variation in Carbon Isotopic Composition of Bog Plant Litter During 3 Years of Field Decomposition.” Biology and Fertility of Soils 46 (1): 73–77. https://doi.org/10.1007/s00374-009-0406-7.
Breeuwer, Angela, Monique Heijmans, Bjorn J. M. Robroek, Juul Limpens, and Frank Berendse. 2008. “The Effect of Increased Temperature and Nitrogen Deposition on Decomposition in Bogs.” Oikos 117 (8): 1258–68. https://doi.org/10.1111/j.0030-1299.2008.16518.x.
Farrish, K. W., and D. F. Grigal. 1985. “Mass Loss in a Forested Bog: Relation to Hummock and Hollow Microrelief.” Canadian Journal of Soil Science 65 (2): 375–78. https://doi.org/10.4141/cjss85-042.
———. 1988. “Decomposition in an Omrotrophic Bog and a Minerotrophic Fen in Minnesota.” Soil Science 145 (5): 353–58. https://doi.org/10.1097/00010694-198805000-00005.
Golovatskaya, E. A., and L. G. Nikonova. 2017. “The Influence of the Bog Water Level on the Transformation of Sphagnum Mosses in Peat Soils of Oligotrophic Bogs.” Eurasian Soil Science 50 (5): 580–88. https://doi.org/10.1134/S1064229317030036.
Hagemann, Ulrike, and Martin T. Moroni. 2015. “Moss and Lichen Decomposition in Old-Growth and Harvested High-Boreal Forests Estimated Using the Litterbag and Minicontainer Methods.” Soil Biology and Biochemistry 87 (August): 10–24. https://doi.org/10.1016/j.soilbio.2015.04.002.
———. 2016. “Data on Moss and Lichen Decomposition Rates and Nutrient Loss from Old-Growth and Harvested High-Boreal Forests Estimated Using the Litterbag and Minicontainer Methods.” Leibniz-Zentrum für Agrarlandschaftsforschung (ZALF) e.V. https://doi.org/10.4228/ZALF.2007.290.
Hiroki, Mikiya, and Makoto M. Watanabe. 1996. “Microbial Community and Rate of Cellulose Decomposition in Peat Soils in a Mire.” Soil Science and Plant Nutrition 42 (4): 893–903. https://doi.org/10.1080/00380768.1996.10416636.
Hogg, Edward H., Victor J. Lieffers, and Ross W. Wein. 1992. “Potential Carbon Losses from Peat Profiles: Effects of Temperature, Drought Cycles, and Fire.” Ecological Applications 2 (3): 298–306. https://doi.org/10.2307/1941863.
Hoorens, Bart, Martin Stroetenga, and Rien Aerts. 2010. “Litter Mixture Interactions at the Level of Plant Functional Types Are Additive.” Ecosystems 13 (1): 90–98. https://doi.org/10.1007/s10021-009-9301-1.
Johnson, Loretta C., and Antoni W. H. Damman. 1991. “Species-Controlled Sphagnum Decay on a South Swedish Raised Bog.” Oikos 61 (2): 234. https://doi.org/10.2307/3545341.
Jones, Matthew, Margaret O’Brien, Bryce Mecum, Carl Boettiger, Mark Schildhauer, Mitchell Maier, Timothy Whiteaker, Stevan Earl, and Steven Chong. 2019. “Ecological Metadata Language Version 2.2.0.” KNB Data Repository. https://doi.org/10.5063/f11834t2.
Lieffers, V. J. 1988. “Sphagnum and Cellulose Decomosition in Drained and Natural Areas of an Alberta Peatland.” Canadian Journal of Soil Science 68 (4): 755–61. https://doi.org/10.4141/cjss88-073.
Limpens, Juul, and Frank Berendse. 2003. “How Litter Quality Affects Mass Loss and N Loss from Decomposing Sphagnum.” Oikos 103 (3): 537–47. https://doi.org/10.1034/j.1600-0706.2003.12707.x.
Mäkilä, M., H. Säävuori, A. Grundström, and T. Suomi. 2018. “Sphagnum Decay Patterns and Bog Microtopography in South-Eastern Finland.” Mires and Peat, no. 21 (July): 1–12. https://doi.org/10.19189/MaP.2017.OMB.283.
Manninen, S., S. Kivimäki, I. D. Leith, S. R. Leeson, and L. J. Sheppard. 2016. “Nitrogen Deposition Does Not Enhance Sphagnum Decomposition.” Science of The Total Environment 571 (November): 314–22. https://doi.org/10.1016/j.scitotenv.2016.07.152.
Müller, Kirill, Jeroen Ooms, David James, Saikat DebRoy, Hadley Wickham, and Jeffrey Horner. 2021. “RMariaDB: Database Interface and ’MariaDB’ Driver.”
Orwin, Kate H., and Nicholas J. Ostle. 2012. “Moss Species Effects on Peatland Carbon Cycling After Fire: Moss Species Effects on C Cycling After Fire.” Functional Ecology 26 (4): 829–36. https://doi.org/10.1111/j.1365-2435.2012.01991.x.
Piatkowski, Bryan T., Joseph B. Yavitt, Merritt R. Turetsky, and A. Jonathan Shaw. 2021. “Natural Selection on a Carbon Cycling Trait Drives Ecosystem Engineering by Sphagnum (Peat Moss).” Proceedings of the Royal Society B: Biological Sciences 288 (1957): 20210609. https://doi.org/10.1098/rspb.2021.0609.
Piatkowski, Bryan, Joseph B. Yavitt, Merritt Turetsky, and A. Jonathan Shaw. 2021. “Online Data for "Natural Selection on a Carbon Cycling Trait Drives Ecosystem Engineering by Sphagnum (Peat Moss).",” August. https://doi.org/10.6084/m9.figshare.14109725.v2.
Pick, Joel L., Shinichi Nakagawa, and Daniel W. A. Noble. 2018. “Reproducible, Flexible and High-Throughput Data Extraction from Primary Literature: The metaDigitise R Package.” https://doi.org/10.1101/247775.
Prevost, Marcel, Pierre Belleau, and André P. Plamondon. 1997. “Substrate Conditions in a Treed Peatland: Responses to Drainage.” Écoscience 4 (4): 543–54. https://doi.org/10.1080/11956860.1997.11682434.
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Sanger, L. J., M. F. Billett, and M. S. Cresser. 1994. “The Effects of Acidity on Carbon Fluxes from Ombrotrophic Peat.” Chemistry and Ecology 8 (4): 249–64. https://doi.org/10.1080/02757549408038552.
Scheffer, R. A., R. S. P Van Logtestijn, and J. T. A. Verhoeven. 2001. “Decomposition of Carex and Sphagnum Litter in Two Mesotrophic Fens Differing in Dominant Plant Species.” Oikos 92 (1): 44–54. https://doi.org/10.1034/j.1600-0706.2001.920106.x.
Scheffer, Robbert A., and Rien Aerts. 2000. “Root Decomposition and Soil Nutrient and Carbon Cycling in Two Temperate Fen Ecosystems.” Oikos 91 (3): 541–49. https://doi.org/10.1034/j.1600-0706.2000.910316.x.
Schieferdecker, Tobias, Kirill Müller, and Darko Bergant. 2022. “dm: Relational Data Models.”
Straková, Petra, Jani Anttila, Peter Spetz, Veikko Kitunen, Tarja Tapanila, and Raija Laiho. 2010. “Litter Quality and Its Response to Water Level Drawdown in Boreal Peatlands at Plant Species and Community Level.” Plant and Soil 335 (1-2): 501–20. https://doi.org/10.1007/s11104-010-0447-6.
Straková, Petra, Timo Penttilä, Jukka Laine, and Raija Laiho. 2012. “Disentangling Direct and Indirect Effects of Water Table Drawdown on Above- and Belowground Plant Litter Decomposition: Consequences for Accumulation of Organic Matter in Boreal Peatlands.” Global Change Biology 18 (1): 322–35. https://doi.org/10.1111/j.1365-2486.2011.02503.x.
Szumigalski, Anthony R., and Suzanne E. Bayley. 1996. “Decomposition Along a Bog to Rich Fen Gradient in Central Alberta, Canada.” Canadian Journal of Botany 74 (4): 573–81. https://doi.org/10.1139/b96-073.
Teickner, Henning, and Klaus-Holger Knorr. 2024. “dpeatdecomposition: R Interface to the Peatland Decomposition Database.” https://github.com/henningte/dpeatdecomposition
Thormann, Markus N, Suzanne E Bayley, and Randolph S Currah. 2001. “Comparison of Decomposition of Belowground and Aboveground Plant Litters in Peatlands of Boreal Alberta, Canada.” Canadian Journal of Botany 79 (1): 9–22. https://doi.org/10.1139/b00-138.
Trinder, Clare J., David Johnson, and Rebekka R. E. Artz. 2008. “Interactions Among Fungal Community Structure, Litter Decomposition and Depth of Water Table in a Cutover Peatland.” FEMS Microbiology Ecology 64 (3): 433–48. https://doi.org/10.1111/j.1574-6941.2008.00487.x.
———. 2009. “Litter Type, but Not Plant Cover, Regulates Initial Litter Decomposition and Fungal Community Structure in a Recolonising Cutover Peatland.” Soil Biology and Biochemistry 41 (3): 651–55. https://doi.org/10.1016/j.soilbio.2008.12.006.
Vitt, Dale H. 1990. “Growth and Production Dynamics of Boreal Mosses over Climatic, Chemical and Topographic Gradients.” Botanical Journal of the Linnean Society 104 (1-3): 35–59. https://doi.org/10.1111/j.1095-8339.1990.tb02210.x.
Waddington, J. M., L. Rochefort, and S. Campeau. 2003. “Sphagnum Production and Decomposition in a Restored Cutover Peatland.” Wetlands Ecology and Management 11 (1): 85–95. https://doi.org/10.1023/A:1022009621693.
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