DOI: 10.5281/zenodo.11276064
title: Peatland Decomposition Database (1.1.0)

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 34 studies, 2,160 litterbag experiments, and 7,297 individual samples with 117,841 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 Updates

Compared to version 1.0.0, this version has a new structure for table experimental_design_format, contains additional metadata on the experimental design (these were omitted in version 1.0.0), and contains the scripts that were used to import the data into the database.




3 Methods



3.1 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 not from all studies that were identified by the literature search data have 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), 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), Asada and Warner (2005), 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), Golovatskaya and Nikonova (2017).





4 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.







5 Attributes
Table 2: Definition of attributes in the Peatland Decomposition Database and entries in the column attribute_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
…
NA
nominal
NA
NA
NA
NA


experimental_design_description
A string describing the variables in the csv file identified by column file in table experimental_design_format for each dataset.
…
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







6 Usage notes



6.1 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), and a folder “scripts” with the R Markdown scripts used to import the data into the database.




6.2 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 dpeatdecomposition < dpeatdecomposition-backup-2025-02-24.sql

Here, <user> is the database user name.




6.3 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).





7 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. “The Peatland Decomposition Database.” 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
Trinder, Johnson, and Artz (2008)


18
Breeuwer et al. (2008)


19
Trinder, Johnson, and Artz (2009)


20
Bragazza and Iacumin (2009)


21
Hoorens, Stroetenga, and Aerts (2010)


22
Straková et al. (2010)


22
Straková et al. (2012)


23
Orwin and Ostle (2012)


24
Lieffers (1988)


25
Manninen et al. (2016)


26
Johnson and Damman (1991)


27
Bengtsson, Rydin, and Hájek (2018a)


27
Bengtsson, Rydin, and Hájek (2018b)


28
Asada and Warner (2005)


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)


34
Golovatskaya and Nikonova (2017)







8 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.

Bona, Kelly Ann, Arlene Hilger, Magdalena Burgess, Nicole Wozney, and Cindy Shaw. 2018. “A Peatland Productivity and Decomposition Parameter Database.” Ecology 99 (10): 2406–6. https://doi.org/10.1002/ecy.2462.

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.

R Core Team. 2022. R: A Language and Environment for Statistical Computing. Manual. Vienna, Austria: R Foundation for Statistical Computing.

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.”

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.