DOI: 10.5281/zenodo.17092587
title: Peatland Mid-Infrared Database (1.0.0)

description:  





README

2025-09-10




Introduction

The peatland mid-infrared database (pmird) stores data from peat, vegetation, litter, and dissolved organic matter samples, in particular mid-infrared spectra and other variables, from previously published and unpublished data sources. The majority of samples in the database are peat samples from northern bogs. Currently, the database contains entries from 26 studies, 11216 samples, and 3877 mid infrared spectra. The aim is to provide a harmonized data source that can be useful to re-analyse existing data, analyze peat chemistry, develop and test spectral prediction models, and provide data on various peat properties.




Usage notes



Download and Setup

The peatland mid-infrared database can be downloaded from https://doi.org/10.5281/zenodo.17092587. The publication contains the following files and folders:





pmird-backup-2025-09-10.sql: A mysqldump backup of the pmird database.




pmird_prepared_data: A folder that contains:



Folders like c00001-2020-08-17-Hodgkins with the raw spectra for samples from each dataset in the pmird database (see below for how to import the spectra).

Files like pmird_prepare_data_c00001-2020-08-17-Hodgkins.Rmd that contain the R code used to process and import the data from each dataset into the database. Corresponding html files contain the compiled scripts.

pmird_prepare_data.Rmd: An Rmarkdown script that was used to run the scripts that created the database (the top level script).





mysql_scripts: A folder that contains:



pmird_mysql_initialization.sql: MariaDB script to initialize the database.

001-db-initialize.Rmd: Rmarkdown script that executes pmird_mysql_initialization.sql and populated dataset-independent tables.

add-citations.Rmd: Rmarkdown script that adds information on references to the database.

add-licenses.Rmd: Rmarkdown script that adds information on licenses to the database.

add-mir-metadata-quality.Rmd Rmarkdown script that adds information on the quality of the infrared spectra to the database.





Dockerfile: A Dockerfile that defines the computing environment used to create the database.




renv.lock A renv.lock file that lists the R packages used to create the database.



The database can be set up as follows: 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 pmird < pmird-backup-2025-09-10.sql

Here, <user> is the database user name.

The database itself does not contain the infrared spectra. These data are in folder pmird_prepared_data which needs to be stored at any place in the file system.





R interface

The R package ‘pmird’ (Teickner 2025) provides an R interface to the database, based on the packages ‘RMariaDB’ (Müller et al. 2021) and ‘dm’ (Schieferdecker, Müller, and Bergant 2022). This interface can also be used to import the mid-infrared spectra that belong to extracted data records (please see the documentation of the ‘pmird’ R package for details, https://henningte.github.io/pmird/).




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 datasets (column reference_publication).

The database can be cited as:



Teickner, H., Agethen, S., Berger, S., Boelsen, R. I., Borken, W., Bragazza, L., Broder, T., De La Cruz, F. B., Diaconu, A.-C., Dise, N. B., Drollinger, S., Estop-Aragonés, C., Gałka, M., Martí, M., Glatzel, S., Groß, J., Harris, L., Heffernan, L., Hodgkins, S. B., … Knorr, K.-H. (2025). Peatland mid-infrared database [Dataset]. https://doi.org/10.5281/zenodo.17092587





Data sources

Data in the database were derived from the following sources: De la Cruz, Osborne, and Barlaz (2016), Hodgkins et al. (2018), Knierzinger et al. (2020), Knierzinger (2020), Münchberger (2019), Münchberger et al. (2019), Schuster et al. (2022), Drollinger, Kuzyakov, and Glatzel (2019), Drollinger et al. (2020), Agethen and Knorr (2018), Kendall (2020), L. I. Harris et al. (2023), L. Harris and Olefeldt (2023), Pelletier et al. (2017), Teickner, Gao, and Knorr (2021), Teickner, Gao, and Knorr (2022), Heffernan (2019), Heffernan et al. (2020), Broder et al. (2012), Anzenhofer (2014), Mathijssen et al. (2019), Wagner (2013), Hömberg (2014), Berger et al. (2017), Berger et al. (2018), Moore et al. (2019), Diaconu et al. (2020), Gałka, Hölzer, et al. (2022), Gałka, Diaconu, et al. (2022), Harris et al. (2018), Harris et al. (2019), Boothroyd et al. (2021), Worrall (2021), Reuter et al. (2019b), Reuter et al. (2019a), Reuter et al. (2020), Liu and Lennartz (2019), Moore et al. (2005), Turunen et al. (2004).




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





Agethen, Svenja, and Klaus-Holger Knorr. 2018. “Juncus Effusus Mono-Stands in Restored Cutover Peat Bogs – Analysis of Litter Quality, Controls of Anaerobic Decomposition, and the Risk of Secondary Carbon Loss.” Soil Biology and Biochemistry 117: 139–52. https://doi.org/10.1016/j.soilbio.2017.11.020.




Anzenhofer, Regina. 2014. “Biogeochemical Characterization of Peat Profiles Along a Vegetation Gradient in an Ombrotrophic Bog, Patagonia.” Master’s thesis.




Berger, Sina, Gerhard Gebauer, Christian Blodau, and Klaus-Holger Knorr. 2017. “Peatlands in a Eutrophic World – Assessing the State of a Poor Fen-Bog Transition in Southern Ontario, Canada, After Long Term Nutrient Input and Altered Hydrological Conditions.” Soil Biology and Biochemistry 114 (November): 131–44. https://doi.org/10.1016/j.soilbio.2017.07.011.




Berger, Sina, Leandra S. E. Praetzel, Marie Goebel, Christian Blodau, and Klaus-Holger Knorr. 2018. “Differential Response of Carbon Cycling to Long-Term Nutrient Input and Altered Hydrological Conditions in a Continental Canadian Peatland.” Biogeosciences 15 (3): 885–903. https://doi.org/10.5194/bg-15-885-2018.




Boothroyd, I. M., F. Worrall, C. S. Moody, G. D. Clay, G. D. Abbott, and R. Rose. 2021. “Sulfur Constraints on the Carbon Cycle of a Blanket Bog Peatland.” Journal of Geophysical Research: Biogeosciences 126 (8). https://doi.org/10.1029/2021JG006435.




Broder, T., C. Blodau, H. Biester, and K. H. Knorr. 2012. “Peat Decomposition Records in Three Pristine Ombrotrophic Bogs in Southern Patagonia.” Biogeosciences 9 (4): 1479–91. https://doi.org/10.5194/bg-9-1479-2012.




De la Cruz, Florentino B., Jason Osborne, and Morton A. Barlaz. 2016. “Determination of Sources of Organic Matter in Solid Waste by Analysis of Phenolic Copper Oxide Oxidation Products of Lignin.” Journal of Environmental Engineering 142 (2): 04015076. https://doi.org/10.1061/(ASCE)EE.1943-7870.0001038.




Diaconu, Andrei-Cosmin, Ioan Tanţău, Klaus-Holger Knorr, Werner Borken, Angelica Feurdean, Andrei Panait, and Mariusz Gałka. 2020. “A Multi-Proxy Analysis of Hydroclimate Trends in an Ombrotrophic Bog over the Last Millennium in the Eastern Carpathians of Romania.” Palaeogeography, Palaeoclimatology, Palaeoecology 538 (January): 109390. https://doi.org/10.1016/j.palaeo.2019.109390.




Drollinger, Simon, Klaus-Holger Knorr, Wolfgang Knierzinger, and Stephan Glatzel. 2020. “Peat Decomposition Proxies of Alpine Bogs Along a Degradation Gradient.” Geoderma 369 (June): 114331. https://doi.org/10.1016/j.geoderma.2020.114331.




Drollinger, Simon, Yakov Kuzyakov, and Stephan Glatzel. 2019. “Effects of Peat Decomposition on δ13C and δ15N Depth Profiles of Alpine Bogs.” CATENA 178 (July): 1–10. https://doi.org/10.1016/j.catena.2019.02.027.







Gałka, Mariusz, Andrei-Cosmin Diaconu, Angelica Feurdean, Julie Loisel, Henning Teickner, Tanja Broder, and Klaus-Holger Knorr. 2022. “Relations of Fire, Palaeohydrology, Vegetation Succession, and Carbon Accumulation, as Reconstructed from a Mountain Bog in the Harz Mountains (Germany) During the Last 6200 Years.” Geoderma 424 (October): 115991. https://doi.org/10.1016/j.geoderma.2022.115991.




Gałka, Mariusz, Adam Hölzer, Angelica Feurdean, Julie Loisel, Henning Teickner, Andrei-Cosmin Diaconu, Marta Szal, Tanja Broder, and Klaus-Holger Knorr. 2022. “Insight into the Factors of Mountain Bog and Forest Development in the Schwarzwald Mts.: Implications for Ecological Restoration.” Ecological Indicators 140 (July): 109039. https://doi.org/10.1016/j.ecolind.2022.109039.




Harris, Lorna I., Tim R. Moore, Nigel T. Roulet, and Andrew J. Pinsonneault. 2019. “Data from: Lichens: A Limit to Peat Growth?” Data. https://doi.org/10.5061/dryad.s136dc8.




———. 2018. “Lichens: A Limit to Peat Growth?” Edited by John Lee. Journal of Ecology 106 (6): 2301–19. https://doi.org/10.1111/1365-2745.12975.




Harris, Lorna I., David Olefeldt, Nicolas Pelletier, Christian Blodau, Klaus-Holger Knorr, Julie Talbot, Liam Heffernan, and Merritt Turetsky. 2023. “Permafrost Thaw Causes Large Carbon Loss in Boreal Peatlands While Changes to Peat Quality Are Limited.” Global Change Biology, August, gcb.16894. https://doi.org/10.1111/gcb.16894.




Harris, Lorna, and David Olefeldt. 2023. “Permafrost Thaw Causes Large Carbon Loss in Boreal Peatlands While Changes to Peat Quality Are Limited.” Dryad. https://doi.org/10.5061/DRYAD.47D7WM3KK.




Heffernan, Liam. 2019. “Peat Carbon, δ14C, Macrofossil, and Humification Data from a Thawing Permafrost Peatland in Western Canada.” UAL Dataverse. https://doi.org/10.7939/DVN/MKM0ZE.










Heffernan, Liam, Cristian Estop-Aragonés, Klaus-Holger Knorr, Julie Talbot, and David Olefeldt. 2020. “Long-Term Impacts of Permafrost Thaw on Carbon Storage in Peatlands: Deep Losses Offset by Surficial Accumulation.” Journal of Geophysical Research: Biogeosciences 125 (3). https://doi.org/10.1029/2019JG005501.




Hodgkins, Suzanne B., Curtis J. Richardson, René Dommain, Hongjun Wang, Paul H. Glaser, Brittany Verbeke, B. Rose Winkler, et al. 2018. “Tropical Peatland Carbon Storage Linked to Global Latitudinal Trends in Peat Recalcitrance.” Nature Communications 9 (1): 3640. https://doi.org/10.1038/s41467-018-06050-2.




Hömberg, Annkathrin. 2014. “Geochemische Charakterisierung von Mooren der Changbai Mountains.” Bachelor thesis, Münster: Münster.




Kendall, Rachel Anne. 2020. “Microbial and Substrate Decomposition Factors in Commercially Extracted Peatlands in Canada.” Master’s thesis, Montréal: McGill University.




Knierzinger, Wolfgang. 2020. “(Bio)Geochemical Data Pürgschachen Moor.” Pangaea.




Knierzinger, Wolfgang, Ruth Drescher-Schneider, Klaus-Holger Knorr, Simon Drollinger, Andreas Limbeck, Lukas Brunnbauer, Felix Horak, Daniela Festi, and Michael Wagreich. 2020. “Anthropogenic and Climate Signals in Late-Holocene Peat Layers of an Ombrotrophic Bog in the Styrian Enns Valley (Austrian Alps).” E&G Quaternary Science Journal 69 (2): 121–37. https://doi.org/10.5194/egqsj-69-121-2020.




Liu, Haojie, and Bernd Lennartz. 2019. “Hydraulic Properties of Peat Soils Along a Bulk Density Gradient-A Meta Study.” Hydrological Processes 33 (1): 101–14. https://doi.org/10.1002/hyp.13314.




Mathijssen, Paul J. H., Mariusz Gałka, Werner Borken, and Klaus-Holger Knorr. 2019. “Plant Communities Control Long Term Carbon Accumulation and Biogeochemical Gradients in a Patagonian Bog.” Science of the Total Environment 684 (September): 670–81. https://doi.org/10.1016/j.scitotenv.2019.05.310.




Moore, Tim, Christian Blodau, Jukka Turunen, Nigel T. Roulet, and Pierre J. H. Richard. 2005. “Patterns of Nitrogen and Sulfur Accumulation and Retention in Ombrotrophic Bogs, Eastern Canada.” Global Change Biology 11 (2): 356–67. https://doi.org/10.1111/j.1365-2486.2004.00882.x.




Moore, Tim R., Klaus-Holger Knorr, Lauren Thompson, Cameron Roy, and Jill L. Bubier. 2019. “The Effect of Long-Term Fertilization on Peat in an Ombrotrophic Bog.” Geoderma 343 (June): 176–86. https://doi.org/10.1016/j.geoderma.2019.02.034.




Müller, Kirill, Jeroen Ooms, David James, Saikat DebRoy, Hadley Wickham, and Jeffrey Horner. 2021. “RMariaDB: Database Interface and ’MariaDB’ Driver.”




Münchberger, Wiebke. 2019. “Past and Present Carbon Dynamics in Contrasting South Patagonian Bog Ecosystems.” PhD thesis, Münster: University Münster.




Münchberger, Wiebke, Klaus-Holger Knorr, Christian Blodau, Verónica A. Pancotto, and Till Kleinebecker. 2019. “Zero to Moderate Methane Emissions in a Densely Rooted, Pristine Patagonian Bog – Biogeochemical Controls as Revealed from Isotopic Evidence.” Biogeosciences 16 (2): 541–59. https://doi.org/10.5194/bg-16-541-2019.




Pelletier, Nicolas, Julie Talbot, David Olefeldt, Merritt Turetsky, Christian Blodau, Oliver Sonnentag, and William L Quinton. 2017. “Influence of Holocene Permafrost Aggradation and Thaw on the Paleoecology and Carbon Storage of a Peatland Complex in Northwestern Canada.” The Holocene 27 (9): 1391–1405. https://doi.org/10.1177/0959683617693899.




Reuter, Hendrik, Julia Gensel, Marcus Elvert, and Dominik Zak. 2019a. “CuO Lignin, and Bulk Decomposition Data of a 75-Day Anoxic Phragmites Australis Litter Decomposition Experiment in Soil Substrates from Three Northeast German Wetlands.” PANGAEA - Data Publisher for Earth & Environmental Science. https://doi.org/10.1594/PANGAEA.902176.




———. 2019b. “Infrared Spectra (FTIR) of Phragmites Australis Litter, Initial and After Anoxic Decomposition in Three Wetland Substrates.” PANGAEA - Data Publisher for Earth & Environmental Science. https://doi.org/10.1594/PANGAEA.902069.




———. 2020. “Evidence for Preferential Protein Depolymerization in Wetland Soils in Response to External Nitrogen Availability Provided by a Novel FTIR Routine.” Biogeosciences 17 (2): 499–514. https://doi.org/10.5194/bg-17-499-2020.




Schieferdecker, Tobias, Kirill Müller, and Darko Bergant. 2022. “dm: Relational Data Models.”




Schuster, Wiebke, Klaus-Holger Knorr, Christian Blodau, Mariusz Gałka, Werner Borken, Verónica A. Pancotto, and Till Kleinebecker. 2022. “Control of Carbon and Nitrogen Accumulation by Vegetation in Pristine Bogs of Southern Patagonia.” Science of the Total Environment 810 (March): 151293. https://doi.org/10.1016/j.scitotenv.2021.151293.




Teickner, Henning. 2025. “pmird: R Interface to the Peatland Mid Infrared Spectra Database.”




Teickner, Henning, Chuanyu Gao, and Klaus-Holger Knorr. 2021. “Reproducible Research Compendium with R Code and Data for: ’Electrochemical Properties of Peat Particulate Organic Matter on a Global Scale: Relation to Peat Chemistry and Degree of Decomposition’.” Zenodo. https://doi.org/10.5281/zenodo.5792970.




———. 2022. “Electrochemical Properties of Peat Particulate Organic Matter on a Global Scale: Relation to Peat Chemistry and Degree of Decomposition.” Global Biogeochemical Cycles 36 (2): e2021GB007160. https://doi.org/10.1029/2021GB007160.




Turunen, Jukka, Nigel T. Roulet, Tim R. Moore, and Pierre J. H. Richard. 2004. “Nitrogen Deposition and Increased Carbon Accumulation in Ombrotrophic Peatlands in Eastern Canada: N Deposition and Peat Accumulation.” Global Biogeochemical Cycles 18 (3). https://doi.org/10.1029/2003GB002154.




Wagner, Sindy. 2013. “Analysis of Peat Decomposition, Element Distribution Patterns and Element Output of Two Peat Bogs in the Thuringian Forest.” Master’s thesis, University Bayreuth.




Worrall, Fred. 2021. “Sulphur Constraints on the Carbon Cycle of a Blanket Bog Peatland [Dataset].” Durham University. https://doi.org/10.15128/R2PK02C9794.