lwf-tea-bag-sites

maintainer: Marcus Schaub

title_for_slug: lwf-tea-bag-sites

en: forest tea-bag roiboos green-tea verification carbon modeling decomposition litter

en: Site Information

en: Descriptive information on sites

en:
Decomposition of plant litter is a key process for the transfer of carbon and nutrients in ecosystems. Carbon contained in the decaying biomass is released to the atmosphere as respired CO2, and may contribute to global warming. Litterbag studies have been used to improve our knowledge of the drivers of litter decomposition, but they lack comparability because litter quality is plant species-specific. The use of commercial tea bags as a standard substrate was suggested in order to harmonize studies, where green tea and rooibos represent more labile and more recalcitrant C compounds as surrogates of local litter.
The tea bag approach was implemented on eight sites of the Swiss long-term Forest Ecosystem Research (LWF) network (https://www.wsl.ch/LWF). This allowed us to take advantage from the existing infrastructure and data from a previous litterbag study with local litter. In Beatenberg and Schaenis, additional elevation transects were established (1200-1800 m and 540-1150 m, respectively) to examine particularly the effect of temperature on decomposition. In Pfynwald (https://www.wsl.ch/de/ueber-die-wsl/versuchsanlagen-und-labors/flaechen-im-wald/pfynwald.html) and Salgesch, infrastructure of running projects was used to examine the effect of drought and understory removal, respectively. In Novaggio, tea bags were incubated in summer and winter to study the effect of seasonality particularly precipitation. Tea bags are collected after 3, 12, 24, and 36 months; for the two time-shifted experiments additionally after 6 and 9 months.
The study has two primary objectives. Firstly, it contributes to TeaComposition initiative (http://teacomposition.org/) which aims at investigating long-term litter decomposition and its key drivers at present as well as under different future climate scenarios using a common protocol and standard litter (tea) across nine terrestrial biomes. Secondly, the data are used to further develop decomposition models such as Yasso (http://en.ilmatieteenlaitos.fi/yasso) which is used by several countries, including Switzerland to estimate the annual carbon fluxes in dead wood, litter, and soil for reporting in National Greenhouse Gas Inventories under the United Nations Framework Convention on Climate Change and the Kyoto Protocol.

carbon

display_name: carbon

decomposition

display_name: decomposition

forest

display_name: forest

green-tea

display_name: green-tea

litter

display_name: litter

modeling

display_name: modeling

roiboos

display_name: roiboos

tea-bag

display_name: tea-bag

verification

display_name: verification

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

en: LWF-Tea bag sites


maintainer: Elisabeth Hafner

en: hazard-mapping natural-hazard satellite snow avalanche

state: active

type: dataset

en: SPOT6 Avalanche Outlines 16 January 2019

en: Shapefile of the manually mapped avalanche outlines. Please only use this data together with the example key document provided with this dataset and within the limitations of the dataset described in the publications.

format: SHP

en:
Outlines of 6'041 avalanches mapped from SPOT6 satellite data over the Swiss Alps on 16 January 2019. The dataset was acquired following a period with very high avalanche danger. The outlines have different attributes described in the data example key (ExampleKey_AvalMapping16012019.pdf)

The generation of the data is described in:

Bühler, Y., E. D. Hafner, B. Zweifel, M. Zesiger, and H. Heisig (2019), Where are the avalanches? Rapid SPOT6 satellite data acquisition to map an extreme avalanche period over the Swiss Alps, The Cryosphere, 13(12), 3225-3238, doi:10.5194/tc-13-3225-2019.

The data was comprehensivly validated in a subset area in

Hafner, E.D.; Techel, F.; Leinss, S.; Bühler, Y., 2021: Mapping avalanches with satellites - evaluation of performance and completeness. Cryosphere, 15, 2: 983-1004. doi: 10.5194/tc-15-983-2021

avalanche

display_name: avalanche

hazard-mapping

display_name: hazard-mapping

natural-hazard

display_name: natural-hazard

satellite

display_name: satellite

snow

display_name: snow

educ

fr: Éducation, culture et sport

de: Bildung, Kultur und Sport

en: Education, culture and sport

it: Istruzione, cultura e sport

envidat

fr: EnviDat: le portail de données environnementales

de: EnviDat: das Umwelt-Datenportal

en: EnviDat: the Environmental Data Portal

it: EnviDat: il portale dei dati ambientali

fr: EnviDat est le portail de données du WSL; il offre un accès uniformisé et réglementé aux données de surveillance et de recherche en matière d’environnement. Ce portail est capable d’héberger et de publier des ensembles de données précieuses et uniques, qui sont partagées aux quatre coins de la planète. Ce faisant, EnviDat favorise la recherche et contribue à l’avancement des sciences environnementales.

de: EnviDat ist das Datenportal der WSL für einen einheitlichen und verwalteten Zugang zu Umweltdaten aus Monitoring- und Forschungsprojekten. Auf dem Portal können Datensätze gehostet und veröffentlicht werden. Durch die weltweite Bereitstellung einzigartiger und wertvoller Datensätze leistet EnviDat einen Beitrag zur Forschung im Bereich der Umweltwissenschaften.

it: EnviDat è il portale dati del WSL che fornisce un accesso unificato e gestito ai dati di monitoraggio ambientale e di ricerca. Il portale ha la capacità di ospitare e pubblicare serie di dati preziosi e unici che vengono condivisi in tutto il mondo. Così facendo, EnviDat promuove la ricerca e contribuisce al progresso della scienza ambientale.

political_level: other

wsl

capacity: public

type: organization

approval_status: approved

key: guid

key: uri

value: Envidat Harvester

en: SPOT6 Avalanche outlines 16 January 2019


greenland-climate-network-gc-net-data

maintainer: EnviDat Support

title_for_slug: greenland-climate-network-gc-net-data

en: greenland aws air-temperature automatic-weather-station net-radiation climate

format: SERVICE

en: GC Net Config for Stations

media_type: application/json

en: Stations Config from the static bucket

format: JSON

en: 22-Petermann ELA

en: Access the latest L1 data

en:
The GC-Net is kindly continued by the Geological Survey of Denmark and Greenland (GEUS).

Starting October 3, 2022, the access to the latest versions of the "ready to use" L1 data has been migrated to GEUS, (doi:10.22008/FK2/VVXGUT). Future versions will be available from GEUS, while the initial version of L1 data has been archived.

en: Archived GC-Net Data (deprecated)

en:
The GC-Net is kindly continued by the Geological Survey of Denmark and Greenland (GEUS).

Starting October 3, 2022, the access to the latest versions of the "ready to use" L1 data has been migrated to GEUS, (doi:10.22008/FK2/VVXGUT). Future versions will be available from GEUS, while the initial versions of L0 and L1 data have been archived.

en: GC Net Chart Parameters

en: Stations parameters from static bucket

en:
In Memory of Dr. Konrad (Koni) Steffen

Update October 2022: The GC-Net is kindly continued by the Geological Survey of Denmark and Greenland (GEUS).
Starting October 3, 2022, the access to the latest versions of the "ready to use" L1 data has been migrated to GEUS. Future data versions will be available at: [https://doi.org/10.22008/FK2/VVXGUT](https://doi.org/10.22008/FK2/VVXGUT)
 Background
Starting with a single station in 1991, the Greenland Climate Network (commonly known as GC-Net) is a set of Automatic Weather Stations (AWS) set up and managed by the late Prof. Dr. Konrad (Koni) Steffen, and spanning the Greenland Ice Sheet (GrIS). This first station was "Swiss Camp" or the "ETH-CU" camp (GC-Net station 01) which was used as a field science and education site by Koni for years. The GC-Net was expanded with multiple NASA, NOAA, and NSF grants throughout the years, and then supported by WSL in the later years. These data (see "C-file" below) were previously hosted by the Cooperative Institute for Research in Environmental Sciences (CIRES) in Boulder, Colorado.

 Overview
Provided in this dataset are the 16 longest running stations in the network, which are spread over a significant area of the GrIS and the majority of the unique climatic zones. From the South Dome high point in the South, to the Western Jakobshavn ablation region in the west, to the Petermann glacier in the North across east of the Northeast Greenland Ice Stream to the east, GC-Net is the longest running climatological record of Greenland.

 The standard GC-Net station consists of:
* Air temperature measurements at 2 heights above the surface
* Temperature and humidity measurements at 2 heights above the surface
* Wind speed and direction measured at 2 heights above the surface
* Sonic distance sounder measurements for 2 snow height and distance of instruments to surface
* Incoming shortwave radiation measurement
* Reflected shortwave radiation measurement
* Net broadband radiation (long- and short-wave) measurement
* Air pressure measurement
Data have often been repatriated in near-real time using one of either the GOES geostationary satellite or the ARGOS polar orbiting satellite transmission system. The stations were visited typically every 1-2 years for maintenance and service, and to download full uncorrupted data directly from the dataloggers. GC-Net stations were visited by Twin Otter equipped with snow skids to land directly on the open-ice at the AWS locations, or by helicopter near the west coast. The AWSs operate on solar and battery power and occasionally lost power during the dark and cold winter months, particularly when the batteries were aging.

 Dataset
This dataset consists of 2 main data levels; Level 0 and Level 1.
Level 0 is the raw data from the dataloggers, historical processing codes, satellite transmissions, and Koni’s personal data archive. Level 0 data (.zip) directories contain subdirectories:
* “C file” - contains the historical processed datafile for each station.
* “Campbell logger files” - contains the raw csv datafiles from the stations’ Campbell Scientific dataloggers since the CR1000 era (~2007-2008 for most stations).
* “Photos” - contains photographs of the station when available marked by year.
Level 1 is the appended, calibrated, cleaned, and quality flagged data. The full processing scheme is open-source and publicly available on the following GitHub repository (please also check GitHub for the latest L1 data):
[GC-Net L1 data on GitHub](https://github.com/GEUS-Glaciology-and-Climate/GC-Net-level-1-data-processing "GC-Net-level-1-data-processing")
Level 1 data is provided in the newly described csv-compatible [NEAD format](https://www.envidat.ch/#/metadata/nead "NEAD format").

 Additional Details
Dataset description publication will be forthcoming.
The Geological Survey of Denmark and Greenland (GEUS) has been imperative in the reprocessing and continuity mission of GC-Net. Multiple GC-Net stations have been replaced with updated and upgraded AWS hardware at the same coordinates by GEUS. This effort will ensure continuity of the GC-Net dataset into the future.

air-temperature

display_name: air-temperature

automatic-weather-station

display_name: automatic-weather-station

aws

display_name: aws

climate

display_name: climate

greenland

display_name: greenland

net-radiation

display_name: net-radiation

en: Greenland Climate Network (GC-Net) Data


maintainer: Franziska Gerber

en: aws python cryowrf antarctica consistent

en: Scripts to preprocess (and download for some databases) atmospheric weather station data. Furthermore, a list of stations and a map can be created to have an overview.

en:
There are many sources providing atmospheric weather station data for the Antarctic continent. However, variable naming, timestamps and data types are highly variable between the different sources. The published python code intends to make processing of different AWS sources from Antarctica easier. For all datasets that are taken into account variables are renamed in a consistent way. Data from different sources can then be handled in one consistent python dictionary.

The following data sources are taken into account:

* AAD: Australian Antarctic Division (https://data.aad.gov.au/aws)
* ACECRC: Antarctic Climate and Ecosystems Cooperative Research Centre by the Australian Antarctic Division
* AMRC: Antarctic Meteorological Research Center (ftp://amrc.ssec.wisc.edu/pub/aws/q1h/)
* BAS: British Antarctic Survey (ftp://ftp.bas.ac.uk/src/ANTARCTIC_METEOROLOGICAL_DATA/AWS/; https://legacy.bas.ac.uk/met/READER/ANTARCTIC_METEOROLOGICAL_DATA/)
* CLIMANTARTIDE: Antarctic Meteo-Climatological Observatory by the italian National Programme of Antarctic Research (https://www.climantartide.it/dataaccess/index.php?lang=en)
* IMAU: Institute for Marine and Atmospheric research Utrecht (Lazzara et al., 2012), https://www.projects.science.uu.nl/iceclimate/aws/antarctica.ph
* JMA: Japan Meteorological Agency (https://www.data.jma.go.jp/antarctic/datareport/index-e.html)
* NOAA: National Oceanic and Atmospheric Administration (https://gml.noaa.gov/aftp/data/meteorology/in-situ/spo/)
* Other/AWS_PE: Princess Elisabeth (PE), KU Leuven, Prof. N. van Lipzig, personal communication
* Other/DDU_transect: Stations D-17 and D-47 (in transect between Dumont d’Urville and Dome C, Amory, 2020)
* PANGAEA: World Data Center (e.g. König-Langlo, 2012)

Important notes

* Information about data sources is available. Some downloading scripts are included in the provided code. However, users should make sure to comply with the data providers terms and conditions.
* Given changing download options of the differnent institutions the above links may not permanently work and data has to be retrieved by the user of this dataset.
* No quality control is applied in the provided preprocessing software - quality control is up to the user of the datasets. Some dataset are quality controlled by the owner.

Acknowledgements
--------------------------
We thank all the data providers for making the data publicly available or providing them upon request. Full acknowledgements can be found in Gerber et al., submitted.

References
---------------
Amory, C. (2020). “Drifting-snow statistics from multiple-year autonomous measurements in Adélie Land, East
Antarctica”. The Cryosphere, 1713–1725. doi: 10.5194/tc-14-1713-2020

Gerber, F., Sharma, V. and Lehning, M.: CRYOWRF - a validation and the effect of blowing snow on the Antarctic SMB, JGR - Atmospheres, submitted.

König-Langlo, G. (2012). “Continuous meteorological observations at Neumayer station (2011-01)”. Alfred Wegener
Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, PANGAEA, doi: 10.1594/PANGAEA.
775173

antarctica

display_name: antarctica

consistent

display_name: consistent

cryowrf

display_name: cryowrf

python

display_name: python

envidat

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

en: Preprocessing Antarctic Weather Station (AWS) data in python


en: xylem-water beech oxygen-isotopes water-isotopes ecohydrology hydrogen-isotopes hydrology forest soil-water cryogenic-extraction fagus-sylvatica spruce picea-abies europe critical-zone isotopes

media_type: text/csv

en: Dataset containing the information on the canopy cover.

format: CSV

media_type: application/zip

format: ZIP

en: Dataset containing information about sample weights, cryogenic water extraction and the actual hydrogen and oxygen isotope data of the study.

en: All canopy pictures in one ZIP file.

en: WATSON_Canopy_Pictures (individual JPG files)

en: All canopy pictures as individual files.

en: Dataset containing the metadata of the sampling sites, including site-, soil-, tree-specific information.

en: Here, we present a comprehensive isotope dataset of soil and stem xylem water collected during two pan-European sampling campaigns in spring and summer 2023. The dataset includes samples from 40 forest sites featuring beech (Fagus sylvatica), spruce (Picea abies), or mixed beech-spruce forests, and is supplemented with detailed site-specific, soil-specific, and tree-specific metadata. Samples and metadata were collected by various researchers across Europe following a standardized protocol. Soil samples were taken at up to five depths (ranging from 0 to 90 cm), and stem xylem samples were collected from three beech and/or spruce trees at each site. All samples were sent to a single laboratory for analysis, where water was extracted using cryogenic vacuum distillation and analyzed with an isotope laser spectrometer. Additionally, a subset of the samples underwent analysis with an isotope ratio mass spectrometer. The complete description of the data can be found in a publication in Earth System Science Data (in review).

beech

display_name: beech

critical-zone

display_name: critical-zone

cryogenic-extraction

display_name: cryogenic-extraction

ecohydrology

display_name: ecohydrology

europe

display_name: europe

fagus-sylvatica

display_name: fagus-sylvatica

forest

display_name: forest

hydrogen-isotopes

display_name: hydrogen-isotopes

hydrology

display_name: hydrology

isotopes

display_name: isotopes

oxygen-isotopes

display_name: oxygen-isotopes

picea-abies

display_name: picea-abies

soil-water

display_name: soil-water

spruce

display_name: spruce

water-isotopes

display_name: water-isotopes

xylem-water

display_name: xylem-water

educ

en: Education, culture and sport

en: EnviDat: the Environmental Data Portal

en: Soil and stem xylem water isotope data from two pan-European sampling campaigns


intratrait

maintainer: Christian Rixen

title_for_slug: intratrait

en: climate-change plant-traits neighbour-interactions cold-adapted-plants elevation-gradient elevation-range

en: Plant trait data along elevation gradients on mountains

en:
This data set was used to test whether species specialized to high elevations or with narrow elevational ranges show more conservative (i.e. less variable) trait responses across their elevational distribution, or in response to neighbours, than species from lower elevations or with wider elevational ranges. We did so by studying intraspecific trait variation of 66 species along 40 elevational gradients in four countries (Switzerland, Australia, New Zealand, China) in both hemispheres. As an indication of potential neighbour interactions that could drive trait variation, we also analysed plant species’ height ratio, its height relative to its nearest neighbour.
The following traits and parameters were measured and are available in this data set:
As an indication of plant stature, we measured vegetative and generative height, where vegetative height was distance from soil to highest vegetative leaf and generative height was distance to the highest point on the reproductive shoot. As a measure of reproductive investment, we noted the presence of flowers on the randomly chosen individuals (see below). As a measure of individual and genet basal area, we measured individual plant and patch diameters, in two dimensions (along the largest diameter and perpendicular to it). In clonal plant species, plant diameter was equivalent to an individual rosette, whereas patch diameter referred to the whole genet and could represent the size of a tuft, tussock or cushion. For genera with more singular growth forms (e.g., some Gentiana species) plant and patch diameter were the same. The two diameter measurements were made at right angles, allowing estimates of patch and plant areas to be calculated as an ellipse (i.e., area = 0.5 a 0.5 b Π). All traits were measured on ten randomly selected individuals per site. Flower count data was considered in a binary fashion on a per individual basis (because for some species individuals only produce one flower when flowering) so that the presence or absence of flower(s) was a nominal value between 0 and 10 for each species at each site. We then collected at least three leaves (up to 30 for small and light leaves) from each of the first three individuals selected from each species for determination of leaf dry matter content (LDMC) and specific leaf area (SLA). For calculations of LDMC and SLA, fresh leaves were scanned on a flatbed scanner to determine leaf area. Leaves were then weighed on a balance to a precision of +/- 0.001g, prior to being air dried and reweighed with a balance to a precision of +/- 0.0001g. LDMC was calculated by dividing dry leaf mass by fresh leaf mass. SLA was calculated by dividing leaf area by dry leaf mass. Additionally, within an area of 10 cm diameter around the target individual, we determined the tallest neighbouring species and measured its vegetative and generative height, and estimated the percent cover of the target species, other vegetation, rock, and bare soil.
For more details see Rixen et al. 2022, Journal of Ecology.

climate-change

display_name: climate-change

cold-adapted-plants

display_name: cold-adapted-plants

elevation-gradient

display_name: elevation-gradient

elevation-range

display_name: elevation-range

neighbour-interactions

display_name: neighbour-interactions

plant-traits

display_name: plant-traits

en: intratrait


maintainer: Chunhong Zhao

en: landscape land-use urban-morphology austin land-dynamics

en: Land use dynamics in Austin since 1992

en: The present dataset is part of the published scientific paper Zhao C, Weng Q, Hersperger A M. Characterizing the 3-D urban morphology transformation to understand urban-form dynamics: a case study of Austin, Texas, USA. Landscape and urban planning, 2020, 203:103881. The overall objective of this paper is to understand urban form dynamics in the Austin metropolitan area for the periods 2006–2011 and 2011–2016. The study also aims to understand to what extent the changes in the built environment (in terms of ‘efficient growth’ versus ‘inefficient growth’) from the 1990s to 2016 in the Austin metropolitan area corresponded with ‘compact and efficient growth’ planning policy documents. The UMT distribution can be found in the paper. The area of transitioning UMT was provided in Table 2 and Table 3 can be found in the Appendix of the paper. A protocol was developed to perform the content analysis of the strategic plans and gather the data. The detailed list of protocol items can be found in Appendix B of the paper. This study demonstrates the advantage of applying Lidar data to characterize 3-D urban morphology type (UMT) transition and understand its dynamics, which helps develop a comprehensive understanding of the urbanization process and provides a tool for planning intentions and policies evaluation on urban development over time. The UMT maps can be found in Appendix A of the paper. The Lidar point datasets and the 30 × 30 m National Land Cover Database (NLCD) are the two main data sources of UMT mapping. Lidar datasets were gathered from different projects that had been conducted and collected by state agencies and other organizations between 2007 and 2017. Table A1 in the appendix in the paper shows the accuracies and acquisition parameters of the Lidar projects from 2007 to 2017. Land use/cover dynamics in Austin metropolitan area dataset provides Land use/cover patterns in the years 1992, 2001, 2004, 2006, 2008, 2011, 2013, 2016 with a spatial resolution of 30 meters. Since NLCD 1992 used a different classification system for the urban land classes, we first reclassified the NLCD 1992 using a customized Arcpy package.

austin

display_name: austin

land-dynamics

display_name: land-dynamics

land-use

display_name: land-use

landscape

display_name: landscape

urban-morphology

display_name: urban-morphology

envidat

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

en: Land use/cover dynamics in Austin metropolitan area since 1992


maintainer: Ueli Reber

en: bgb policy-documents policy-analysis text-corpus switzerland biodiversity environmental--policy

en: Replication files

en:
 Introduction

The ZIP file contains all data and code to replicate the analyses reported in the following paper.

Reber, U., Fischer, M., Ingold, K., Kienast, F., Hersperger, A. M., Grütter, R., & Benz, R. (2022). Integrating biodiversity: A longitudinal and cross-sectoral analysis of Swiss politics. *Policy Sciences*. [https://doi.org/10.1007/s11077-022-09456-4](https://doi.org/10.1007/s11077-022-09456-4)

If you use any of the material included in this repository, please refer to the paper. If you use (parts of) the text corpus, please also refer to the sources used for its compilation listed below. The content of the texts may not be changed.

 Data folder

The data folder contains the following files.

* _corpus.parquet_: Text corpus of Swiss policy documents
* _dict_de.csv_: Biodiversity dictionary (German)
* _dict_fr.csv_: Biodiversity dictionary (French)
* _dict_it.csv_: Biodiversity dictionary (Italian)
* _topic_labels.csv_: labels/codes for policy sectors
* _topics.csv_: labels/codes for policy sectors

The corpus and the dictionary were compiled by the authors specifically for this project. The labels/codes for policy sectors are based on the [coding scheme](http://ws-old.parlament.ch/affairs/topics) of the Swiss Parliament.

 Text corpus

The text corpus consists of 439,984 Swiss policy documents in German, French, and Italian from 1999 to 2018. The corpus was compiled from the following source between 2020-10-01 and 2021-01-31.

* Transcripts and parliamentary businesses (e.g. questions, motions, parliamentary initiatives) via the [Web Services (WS)](https://www.parlament.ch/de/%C3%BCber-das-parlament/fakten-und-zahlen/open-data-web-services) provided by the Swiss Parliament
* The official compilation of federal legislation ("Amtliche Sammlung", AS) via [opendata.swiss](https://opendata.swiss/de/dataset/official-compilation-of-federal-legislation-bs-as-1947-2018) provided by the Swiss Federal Archives (SFA)
* The federal gazette ("Bundesblatt") via [fedlex.admin.ch](https://www.fedlex.admin.ch/de/fga/index)
* Decisions of federal courts via [entscheidsuche.ch (ES)](https://entscheidsuche.ch/)

The corpus is stored in a single data frame to use with R saved as [PARQUET](https://parquet.apache.org/) file (corpus.parquet). The data frame has the following structure.

* _text_id_: Unique identifier for each text (source information as prefix, e.g. "t_")
* _doc_type_: Document type (see coding scheme below)
* _branch_: Government branche (1 legislative, 2 executive, 3 judicative)
* _stage_: Stage of policy process (1 drafting, 2 introduction, 3 interpretation)
* _year_: Year of publication
* _topic_: Policy sector (coding scheme in separate file in data folder)
* _lang_: Language (de, fr, it)
* _text_: Text

The following list contains the coding scheme for the doc_type variable.

* 101: Federal gazette // Draft for public consultation ("Vernehmlassungsverfahren")
* 102: Federal gazette // Explanation of draft for parliament ("Botschaft")
* 103: Federal gazette // Strategy, action plan
* 104: Federal gazette // Federal council decree ("Bundesratsbeschluss")
* 105: Federal gazette // (Simple) Federal decree ("(Einfacher) Bundesbeschluss")
* 106: Federal gazette // General decree ("Allgemeinverfügung")
* 107: Federal gazette // Treaty ("Übereinkommen")
* 108: Federal gazette // Treaty ("Abkommen")
* 109: Federal gazette // Draft for parliament ("Entwurf")
* 110: Federal gazette // Report ("Bericht")
* 111: Federal gazette // Report of parliamentary comission ("Bericht")
* 112: Federal gazette // Report of federal council ("Bericht")
* 201: Parl. businesses // Submitted text
* 202: Parl. businesses // Reason text
* 203: Parl. businesses // Federal council response
* 204: Parl. businesses // Initial situation
* 205: Parl. businesses // Proceedings
* 301: Parl. transcripts // Speech of MP
* 302: Parl. transcripts // Speech of federal council
* 401: Federal legislation // Legal text of the official compilation (law, ordinances, etc.)
* 501: Court decisions // Federal Supreme Court
* 502: Court decisions // Federal Criminal Court
* 503: Court decisions // Federal Administrative Court

 Code folder

The code folder contains all R code for the analyses. The files are numbered chronologically.

* _1_classifier_training.R_: Training of classifiers for classification of policy sectors
* _2_classifier_application.R_: Classification of documents in corpus
* _3_dictionary_application.R_: Biodiversity indexing of documents in corpus
* _4_stm_truncation.R_: Truncation of indexed documents to keep only relevant parts
* _5_stm_translation.R_: Translation of FR and IT documents to DE
* _6_stm_model.R_: Preprocesssing and structural topic model
* _7_plots.R_: Plots and numbers as included in the paper

The code/functions folder contains custom functions used in the scripts, e.g. to support topic model interpretation.

Package versions and setup details are noted in the code files.

 Contact

Please direct any questions to Ueli Reber (ueli.reber@eawag.ch).

bgb

display_name: bgb

biodiversity

display_name: biodiversity

environmental--policy

display_name: environmental--policy

policy-analysis

display_name: policy-analysis

policy-documents

display_name: policy-documents

switzerland

display_name: switzerland

text-corpus

display_name: text-corpus

en: Replication files for "Integrating biodiversity: A longitudinal and cross-sectoral analysis of Swiss politics"


maintainer: Matthias Haeni

en: par meteo relative-humidity long-term temperature climate-change swiss-forest-lab meteorology precipitation wind-speed

en: Site aerial photo (Jussy)

en: Site aerial photo from both Jussy stations. Source: Google. 2016. Site aerial photo from both Jussy stations. Retrieved November 11, 2016, from https://www.google.ch/maps

mimetype: image/jpeg

en: Forest station data (JUB)

en: Data file.

mimetype: text/csv

en: Data plot of the field station (JUF)

en: Data plot of the forest station (JUB)

media_type: application/pdf

en: Data overview for air temperature, relative humidity, precipitation, PAR, wind speed.

format: PDF

mimetype: application/pdf

en: Site photo of the forest station (JUB)

en: Site photo of the forest station from the side.

en: Site photo of the field station (JUF)

en: Site photo of the field station from the side.

en: High quality meteorological data are needed for long-term forest ecosystem research, particularly in the light of global change. The long-term data series published here comprises almost 20 years of measurements for two meteorological stations in Jussy in Switzerland where one station is located within a natural broad-leaved forest stand (JUB) with sessile oak (_Quercus petrea_; 90 yrs), aspen (_Populus tremula_; 60 yrs) and European hornbeam (_Carpinus betulus_; 60 yrs) as dominant tree species. A second station is situated in the very vicinity outside of the forest (field station, JUF). The meteorological time series are presented in hourly time resolution of air temperature, relative humidity, precipitation, photosynthetically active radiation (PAR) and wind speed. Jussy is part of the Long-term Forest Ecosystem Research Programme (LWF) established and maintained by the Swiss Federal Research Institute WSL.

climate-change

display_name: climate-change

long-term

display_name: long-term

meteo

display_name: meteo

meteorology

display_name: meteorology

par

display_name: par

precipitation

display_name: precipitation

relative-humidity

display_name: relative-humidity

swiss-forest-lab

display_name: swiss-forest-lab

temperature

display_name: temperature

wind-speed

display_name: wind-speed

en: Jussy, Switzerland: Long-term forest meteorological data from the Long-term Forest Ecosystem Research Programme (LWF), from 1997 onwards


maintainer: Ionut Iosifescu Enescu

en: reproducibility open-source hpc jupyter-notebooks open-science research-data-management open-data

en: Open Science Support @ WSL (Poster)

en:
This poster was originally created for the swissuniversities Open Science Action Plan: Kick-Off Forum, and showed to the audience on 17.10.2019. It illustrates how the environmental data portal EnviDat provides the tools for fostering Open Science and Reproducibility of scientific research at WSL.

Supporting open science is a highly relevant user requirement for EnviDat and for implementing FAIR (Findability, Accessibility, Interoperability and Reusability) principles at dataset level.
EnviDat encourages WSL scientists to complement data publication with a complete description of research methods and the inclusion of the open source software, code or scripts used for processing the dataset or for obtaining the published results. By openly publishing open software (e.g. as Jupyter notebooks) alongside research data sets, researchers can contribute to mitigate reproducibility issues.

EnviDat also promotes and supports, where possible and practical, the publication of software as Jupyter notebooks. Jupyter notebooks provide a solution for improved documentation and interactive execution of open code in a wide range of programming languages (Python, R, Octave/Matlab, Java or Scala). These programming languages are widely used in environmental research at WSL and well supported by the Jupyter-compatible kernels. We have sucessfully interfaced EnviDat-hosted notebooks with the WSL High-Performance Computing (HPC) Linux Cluster through a JupyterHub/JuypterLab beta installation on the HPC cluster implemented in close collaboration with the WSL IT-Services.
For existing software that cannot be easily migrated to Jupyter Notebooks, the Open Science and Reproducibility is assisted by containerisation. We have proven that several Singularity containers can successfully run on WSL's HPC cluster.

Finally, the researchers can upload the data/results complemented by code (e.g. as Jupyter Notebooks, or Singularity containers) and any additional documentation in EnviDat. Consequently, they will receive a DOI for the entire dataset, which they can reference in their science paper in order to publish a more reproducible research.

_License_: This poster is released by WSL and the EnviDat team to the public domain under a Creative Commons 4.0 CC0 "No Rights Reserved" international license. You can reuse this poster in any way you want, for any purposes and without restrictions.

hpc

display_name: hpc

jupyter-notebooks

display_name: jupyter-notebooks

open-data

display_name: open-data

open-science

display_name: open-science

open-source

display_name: open-source

reproducibility

display_name: reproducibility

research-data-management

display_name: research-data-management

educ

en: Education, culture and sport

envidat

en: EnviDat: the Environmental Data Portal

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

en: Open Science Support at the Swiss Federal Research Institute WSL. The EnviDat Concept


en: snow-mechanics snow microstructure x-ray-tomography compression-experiments

en: Snowmicroquakes Data

en: Compression experiments, X-ray images and simulation data with supplemented README file

en:
When snow is compressed with a certain speed, micro-snowquakes are triggered in the porous structure of bonded crystals. The present dataset covers uniaxial compression experiments of snow at different strain rates and concurrent X-ray tomography imaging documenting this feature.

The experiments were conducted in a micro-compression stage operated in the X-ray tomography scanner in the SLF cold laboratory. The dataset comprises the compression force data of 17 compression experiments, the 3D image data from 4 X-ray tomography scans and the results of numerical simulations.

compression-experiments

display_name: compression-experiments

microstructure

display_name: microstructure

snow

display_name: snow

snow-mechanics

display_name: snow-mechanics

x-ray-tomography

display_name: x-ray-tomography

en: Compressive stick slip and snow-micro-quakes


digitizing-historical-plague

maintainer: Christian Ginzler

title_for_slug: digitizing-historical-plague

en: palaeo-epidemiology plague-mapping plague-inventory yersinia-pestis historical-plague black-death bubonic-plague plague-outbreaks

en: We present newly digitized data on 6,929 plague outbreaks that occurred between 1347 and 1900 AD across Europe. The data base on an inventory initially published 1976. For georeferencing the information of Tele Atlas 2009 was used. The coordinates are in the reference systems ETRS89 and WGS84.

mimetype: application/zip

black-death

display_name: black-death

bubonic-plague

display_name: bubonic-plague

historical-plague

display_name: historical-plague

palaeo-epidemiology

display_name: palaeo-epidemiology

plague-inventory

display_name: plague-inventory

plague-mapping

display_name: plague-mapping

plague-outbreaks

display_name: plague-outbreaks

yersinia-pestis

display_name: yersinia-pestis

en: Digitizing historical plague


maintainer: Anita C Risch

en: climate anthropogenic-management microbial-respiration nutrient-addition soil-properties microbial-biomass-carbon herbivore-exclusion

en: Risch et al. GEB_data.xlsx

en:
Study sites and experimental design
We collected data from 23 sites that are part of the Nutrient Network Global Research Cooperative (NutNet, https://nutnet.umn.edu/). The mean annual air temperature (MAT) across these sites ranged from -4 to 22°C, mean annual precipitation (MAP) from 252 to 1592 mm, and elevations from 6 to 4261 m above sea level (Fig 1a, Supplementary Table S1), hence cover a wide range of climatic conditions under which grasslands occur (Fig 1b). Soil organic C concentrations ranged between 0.8 to 7.8%, soil total N concentrations between 0.1 and 0.6%, and the soil C:N ratio between 9.1 and 21.5. Soil clay content spanned from 3.0 to 35%, and soil pH from 3.4 to 7.6 (Supplementary Table S2).
At each site, the effects of nutrient addition and herbivore exclusion were tested via a randomized-block design (Borer et al., 2014). Three blocks with 10 treatment plots each were established at each site, except for the site at bldr.us (only two blocks). Each of these 10 plots was randomly assigned to a nutrient or fencing treatment. An individual plot was 5 x 5 m, divided into four 2.5 x 2.5 m subplots. Each subplot was further divided into four 1 x 1 m square sampling plots, one of which was set aside for soil sampling (Borer et al., 2014). Plots were separated by at least 1 m wide walkways. We collected soil samples from four different treatments for this study: (i) untreated control plots (Control), (ii) herbivore exclusion plots (Fence), (iii) plots fertilized with N, P, K, plus nine essential macro and micronutrients (NPK), and (iv) plots with simultaneous fertilizer addition and herbivore exclusion (NPK+Fence). The experiments were established at different times in the past, with years of treatment different among sites (2 – 9 years since start of treatment; Supplementary Table S1). For the nutrient additions, all sites applied 10 g N m-2 each year as time-release urea; 10 g P m-2 yr-1 as triple-super phosphate; 10 g K m-2 yr-1 as potassium sulfate. A micro-nutrient mix (Fe, S, Mg, Mn, Cu, Zn, B, Mo, Ca) was applied at 100 g m-2 together with K in the first year of treatments but not thereafter.
We excluded large vertebrate herbivores (Fence) by fencing two plots, one with and one without NPK additions, within each block. The fences excluded all aboveground mammalian herbivores with a body mass of over 50 g (Borer et al., 2014). At most sites, the fences were 180 cm high, and the fence contained a wire mesh (1 cm holes) for the bottom 90 cm with a 30 cm outward-facing flange stapled to the ground to exclude burrowing animals. Climbing and subterranean animals may potentially still access these plots (Borer et al., 2014). For slight modifications in fence design at a few sites see Supplementary Table S3. Most sites only had wild herbivores, although four sites were also grazed by domestic animals (Supplementary Table S1).

Collection of soil samples, soil microbial respiration, microbial biomass, and other soil properties
Each of the 23 sites received a package containing identical material from the Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Switzerland to be used for sampling (Risch et al., 2015; Risch et al., 2019). We collected two soil cores of 5 cm diameter and 12 cm depth in each sampling plot and composited them to measure MR, MBC, and soil chemical properties (see below). An additional sample (5 x 12 cm) was collected to assess soil physical properties. This sample remained within a steel sampling core after collection and both ends were tightly closed with plastic caps to avoid disturbance. All soils were shipped cooled to the laboratory at (Location will be disclosed after manuscript acceptance) within a few days after collection. Soils were sampled roughly 6 weeks prior to peak biomass at each site during 2015 and 2016.
To assess MR (CO2 production) in a laboratory incubation experiment we weighed duplicate soil samples (8 g dry soil equivalent) into 50-ml Falcon tubes. No additional substrate (glucose, sugar) was added to these samples. We adjusted the soil moisture of each sample to 60% field capacity. We then placed a 15 ml plastic test tube (Semadeni 1701A) containing 7.25 ml 0.05 M NaOH over each soil sample. The test tube was fixed with a plastic rod so that it was not in contact with the soil sample. The Falcon tubes were then sealed with a screw cap and placed in an incubator under completely dark conditions at 20°C. The CO2 produced by microbial respiration was absorbed by the 0.05 M NaOH. For five weeks we measured the decrease in conductivity within the 0.05 M NaOH solution on a weekly basis with a Multimeter WTW Multi 3410 (WTW GmbH, Germany) and replaced the 0.05 M NaOH with fresh solution. We included Falcon tubes without soil samples in each incubation run as blanks to test if tubes were tight and no CO2 could enter or escape. We calibrated the relationship between conductivity reduction and NaOH absorbed as follows: 400 ml 0.05 M NaOH was placed in a beaker and its conductivity was measured with the multimeter. While stirring, air containing CO2 was blown into the solution for approximately one minute, which reacts with NaOH to form Na2CO3. After this process, conductivity was measured again. We then transferred 7.25 ml of the solution into a smaller beaker and added 1 ml of 0.1 M BaCl2 to precipitate Na2CO3 and then titrated the solution with 0.05 M HCl to determine the remaining NaOH. We then repeated these steps with the remaining solution a total of nine times and plotted the conductivities (y-axis) against the NaOH consumed (x-axis, Supplementary Fig S1). This regression line was used to infer the consumption of NaOH from the conductivity reduction in the incubation experiments and to calculate CO2 evolution during incubation. In addition, we determined the optimum concentration for the NaOH solution in series of preliminary experiments, so that the concentration was not too high to become insensitive, but also not too low so that not all NaOH reacts during incubation. We then calculated MR (mg CO2-C kg dry soil-1 h-1) as total amount of CO2 released over the 5 weeks divided by the duration of the entire incubation in hrs.
Soil microbial biomass carbon (MBC; mg C kg soil-1 ) was measured at the beginning of the experiment by measuring the maximal respiratory response to the addition of glucose solution (4 mg glucose per g soil dry weight dissolved in distilled water; substrate-induced respiration method) on approximately 5.5 g of soil (J. P. E. Anderson & Domsch, 1978; Nico Eisenhauer et al., 2018; Scheu, 1992). For this purpose we used an O2-micro-compensation apparatus (Scheu, 1992). More specifically, substrate-induced respiration was calculated from the respiratory response to D-glucose for 10 hr at 20°C. Glucose was added according to preliminary studies to saturate the catabolic enzymes of microorganisms (4 mg g soil-1 dissolved in 400 ml deionized water). The mean of the lowest three readings within the first 10 hrs (between the initial peak caused by disturbing the soil and the peak caused by microbial growth) was taken as maximum initial respiratory response (MIRR; ml O2 kg soil-1 h-1) and microbial biomass (mg C kg soil-1) was calculated as 38 x MIRR (Beck et al., 1997; Cesarz et al., 2022; Thakur et al., 2015).
The rest of the composited sample was dried at 65°C for 48 h, ground and sieved (2 mm mesh) to assess the soil pH, mineral soil total C and N and C:N ratio, and mineral soil organic C (Risch et al., 2019). The undisturbed sample was used to assess water holding capacity (WHC), bulk density (BD), and soil texture [sand, silt, clay; methods in (Risch et al., 2019)]. We used the percentage of sand and clay as an indicator of soil texture in this study. MAT (°C), MAP (mm) and temperature of the wettest quarter (°C) were obtained from www.worldclim.com (Fick & Hijmans, 2017; Hijmans, Cameron, Parra, Jones, & Jarvis, 2005). These variables were selected as they were found to be drivers of soil nutrient processes across these sites in earlier studies (Risch et al., 2020; Risch et al., 2019). Mean annual soil temperatures (MAST; °C) for the 0 to 5 cm soil layer were obtained for each site from the SoilTemp maps (J. Lembrechts et al., 2021; J. J. Lembrechts et al., 2022), global gridded modelled products of soil bioclimatic variables for the 1979-2013 period at a 1-km² resolution, based on CHELSA, ERA5 and in-situ soil temperature measurements.
Numerical calculations and statistical analyses
We calculated MMQ as MR/MBC. We corrected this measure using the average soil temperature of each site (MMQsoil). This temperature correction is necessary as incubation temperatures are usually much higher than site mean annual soil temperatures (see Xu et al. 2017). MMQsoil = MMQ x Q10(MAST – 20)/10, where Q10 was assumed to be 2 (Xu et al. 2017). See Supplementary Fig S2 for comparison of air and soil temperatures across the 23 sites as well as the incubation temperature.
Some of the explanatory variables (clay, soil organic C, C:N ratio) were skewed and were thus log-transformed prior to analyses. All continuous explanatory variables were centred and scaled to have a mean of zero and variance of one. To avoid collinearity between them we filtered them using correlation analysis (Supplementary Fig S3). From the variables that were strongly correlated (Pearson’s |r| > 0.70) (Dormann et al., 2013), we selected the ones that allowed us to minimize the number of variables (Supplementary Fig S3). Specifically, soil total N concentration, soil total C concentration, soil sand content and soil bulk density were dropped from the dataset. We then assessed how these edaphoclimatic variables are related to MMQ across our global grasslands.
For this, we used linear mixed effects models (LMMs) fitted by maximum likelihood with the lme function in the nlme package (version 3.1-153) (Pinheiro, Bates, DebRoy, & Sarkar, 2021) in R version 3.6.3. (R Core Team, 2019). We used treatment as a fixed effect and plot nested in site as random effects to assess treatment differences in MMQsoil, as well as MR, and MBC. The number of years since the treatment started was included as a fixed effect in all the initial models but was not significant and therefore not retained in the models. To assess how differences in MMQsoil were affected by environmental factors (soil, climatic properties) we again used LMMs. Soil and climatic properties were included as fixed effects and plot nested in site as random effects. We did not include interactions between environmental variables. We then used the MuMin package (Barton, 2018) (version 1.42.1) to select the best models that explained the most variation based on Akaike’s information criterion (AIC; model.avg function). We used the corrected AIC (AICc) to account for our small sample size and selected the top models that fell within 4 AICc units (delta AICc < 4) (Burnham & Anderson, 2002; Johnson & Omland, 2004). We present all our top models rather than model averages. Conditional averages are provided in the Supplementary material.
Based on findings from analyses described above and the literature, we developed a conceptual model of direct and indirect relationships between both edaphoclimatic variables and experimental treatments (Supplement Figure S4) to obtain a more holistic approach in understanding how these properties affect MMQsoil. We had data from 23 sites with 272 observations. We tested this model using structural equation modelling based on a d-sep approach (Lefcheck, 2016; Shipley, 2009). We considered those environmental drivers that were included in our top LMMs, namely temperature of the wettest quarter (T.q.wet), soil pH, water holding capacity (WHC) and soil organic C (organic C; Supplementary Figure S4). These factors were allowed to directly affect MMQsoil, and via their interactions with treatments. In addition, treatments were allowed to directly affect MMQsoil. Treatments were included as dummy variables in the model. We tested our conceptual model (Supplementary Fig S4) using the piecewiseSEM package (version 2.0.2; Lefcheck, 2016) in R 3.4.0, in which a structured set of linear models are fitted individually. This approach allowed us to account for the nested experimental design, and overcome some of the limitations of standard structural equation models, such as small sample sizes (Lefcheck, 2016; Shipley, 2009). We used the lme function of the nlme package to model response variables, including site as a random factor. Good fit of the SEM was assumed when Fisher’s C values were non-significant (p > 0.05). For all significant interactions between soil or climate variables and treatments detected in the SEMs, we calculated treatment effect sizes, i.e., the differences in MMQsoil between Control and treatments as log response ratios (LRR) and plotted these values against the climate or soil factors. The LRR were defined as log(Control/Treatment), where treatment was either Fence, NPK or NPK+Fence. To assess which of the LRR-climate or soil property relationships were significant we again used LMMs, in which soil and climatic properties were included as fixed effects and plot nested in site as random effects.

en:
This dataset contains all data on which the following publication below is based.

Paper Citation:

Risch Anita C., Zimmermann, Stefan, Schütz, Martin, Borer, Elizabeth T., Broadbent, Arthur A.D., Caldeira, Maria C., Davies, Kendi F., Eisenhauer, Nico, Eskelinen, Anu, Fay, Philip A., Hagedorn, Frank, Knops, Johannes M.H., Lembrechts, Jonas, J., MacDougall, Andrew S., McCulley, Rebecca L., Melbourne, Brett A., Moore, Joslin L., Power, Sally A., Seabloom, Eric W., Silveira, Maria L., Virtanen, Risto, Yahdjian, Laura, Ochoa-Hueso, Raul (accepted). Drivers of the microbial metabolic quotient across global grasslands. Global Ecology and Biogeography

Please cite this paper together with the citation for the datafile.

The microbial metabolic quotient (MMQ; mg CO2-C mg MBC-1 h-1), defined as the amount of microbial CO2 respired (MR; mg CO2-C kg soil-1 h-1) per unit of microbial biomass C (MBC; mg C kg soil-1), is a key parameter for understanding the microbial regulation of the carbon (C) cycle, including soil C sequestration. Here, we experimentally tested hypotheses about the individual and interactive effects of multiple nutrient addition (NPK+micronutrients) and herbivore exclusion on MR, MBC, and MMQ across 23 sites (5 continents). Our sites encompassed a wide range of edaphoclimatic conditions, thus we assessed which edaphoclimatic variables affected MMQ the most and how they interacted with our treatments. Soils were collected in plots with established experimental treatments. MR was assessed in a five-week laboratory incubation without glucose addition, MBC via substrate-induced respiration. MMQ was calculated as MR/MBC and corrected for soil temperatures (MMQsoil). Using LMMs and SEMs, we analysed how edaphoclimatic characteristics and treatments interactively affected MMQsoil. MMQsoil was higher in locations with higher mean annual temperature, lower water holding capacity, and soil organic C concentration, but did not respond to our treatments across sites as neither MR nor MBC changed. We attributed this relative homeostasis to our treatments to the modulating influence of edaphoclimatic variables. For example, herbivore exclusion, regardless of fertilization, led to greater MMQsoil only at sites with lower soil organic C (<1.7%). Our results pinpoint the main variables related to MMQsoil across grasslands and emphasize the importance of the local edaphoclimatic conditions in controlling the response of the C cycle to anthropogenic stressors. By testing hypotheses about MMQsoil across global edaphoclimatic gradients, this work also helps to align the conflicting results of prior studies.

anthropogenic-management

display_name: anthropogenic-management

climate

display_name: climate

herbivore-exclusion

display_name: herbivore-exclusion

microbial-biomass-carbon

display_name: microbial-biomass-carbon

microbial-respiration

display_name: microbial-respiration

nutrient-addition

display_name: nutrient-addition

soil-properties

display_name: soil-properties


en: electrical-conductivity groundwater topsoil-interflow studibach overland-flow plot stable-isotopes soil-water rainfall alptal

en:
This dataset contains stable isotope ratios of oxygen and hydrogen (O-18 and H-2) and electrical conductivity (EC) in overland flow (OF), topsoil interflow (TIF), soil water, groundwater, and rainwater for 12 rainfall events during the snow-free seasons of 2021 and 2022 in the Studibach catchment, Alptal, Switzerland.

Overland flow, topsoil interflow (i.e., lateral flow from the more densely rooted soil layer), soil water, and groundwater were collected at 14 small trenched runoff plots (1 x 3 m) in three subcatchments (C2, C3, C5) of the Studibach catchment. Overland flow was collected from the surface up to 2-5 cm depth and thus includes biomat flow. A trench was used to collect topsoil interflow (up to 60 cm below the surface; see Table 1 in the manuscript for details). Rainwater was collected at two locations in the Studibach catchment (in C3 and C5, respectively). Soil water was collected in between the events from suction lysimeters installed at 12.5 cm and 20 cm below the soil surface in the middle of each plot. Groundwater was collected between events from wells installed near the plots up to the soil-bedrock interface.
The water samples were analysed for the stable isotopes of oxygen and hydrogen (O-18 and H-2) using with a cavity ring-down spectroscope (CRDS; L2140-i or L2130-i, Picarro, Inc., USA) at the Chair of Hydrology at the University of Freiburg, Germany. The isotope ratios are reported in per mil (‰) relative to Vienna Standard Mean Ocean Water.

A more detailed description of the field setup, data collection and preparation can be found in Leuteritz et al. (in press).

The dataset contains in addition to the sample identifier and the site and event identifiers that are used in the publication, also the sample collection date (typically one day after the event) and the coordinates for each plot (coordinate system: WGS84). For the plots for which samples were collected with an automatic sampler (ISCO), the date and time (UTC) of sample collection are given as well.

alptal

display_name: alptal

electrical-conductivity

display_name: electrical-conductivity

groundwater

display_name: groundwater

overland-flow

display_name: overland-flow

plot

display_name: plot

rainfall

display_name: rainfall

soil-water

display_name: soil-water

stable-isotopes

display_name: stable-isotopes

studibach

display_name: studibach

topsoil-interflow

display_name: topsoil-interflow

en: Stable water isotopes and EC in overland flow, topsoil interflow, soil water, groundwater, and rainwater for 12 rainfall events in the Studibach catchment, Alptal, Switzerland


maintainer: Avalanche Warning Service SLF

en: Avalanche fatalities per year in Switzerland since 1936/1937

en:
Attention: this data is not updated after 2022 anymore.
This dataset contains the statistics on the number of avalanche fatalities per hydrological year in Switzerland. The data set commences with the beginning of the hydrological year 1936/37 on 01/10/1936. After the completion of a hydrological year, the new data is appended to the existing dataset.
The following information is contained (by column and column title):
 - hydrological year
 - number of fatalities in the backcountry (=tour)
 - number of fatalities in terrain close to ski areas (=offpiste)
 - number of fatalities on transportation corridors including ski runs, roads, railway lines (=transportation.corridors)
 - number of fatalities in or around buildings or in settlements (= buildings)
 - sum (of all four categories)
The definition for these four categories as described in the guidelines to the avalanche accident database:
**tour**:
activities include back-country ski, snowboard or snow-shoe touring
**offpiste**:
access from ski area, generally from the top of a skilift with short hiking distances
**transportation.corridors** ([Techel et al., 2016](http://www.geogr-helv.net/71/147/2016/ )):
people travelling or recreating on open or temporarily closed
transportation corridors (e.g. a road user or a skier on a ski run) and people working on open or closed transportation corridors (e.g. maintenance crews on roads, professional rescue teams)
**buildings** ([Techel et al., 2016](http://www.geogr-helv.net/71/147/2016/ )):
people inside or just outside buildings, and workers on high alpine building
sites

avalanche-accident-statistics

display_name: avalanche-accident-statistics

avalanche-accidents

display_name: avalanche-accidents

avalanche-fatalities

display_name: avalanche-fatalities

fatalities-in-or-around-buildings

display_name: fatalities-in-or-around-buildings

fatalities-in-settlements

display_name: fatalities-in-settlements

fatalities-in-the-backcountry

display_name: fatalities-in-the-backcountry

fatalities-on-transportation-corridors

display_name: fatalities-on-transportation-corridors

educ

en: Education, culture and sport

envidat

en: EnviDat: the Environmental Data Portal

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

en: Number of avalanche fatalities per hydrological year in Switzerland since 1936-1937


weissfluhjoch-dataset-for-esm-snowmip

maintainer: Nander Wever

title_for_slug: weissfluhjoch-dataset-for-esm-snowmip

en: esm-snowmip snow snow-depth weissfluhjoch snow-models

en: ini file

en: This ini file is required by data-converter from MeteoIO version 1887 (http://models.slf.ch/p/meteoio/)

en: Dataset Weissfluhjoch for ESM-SnowMIP

en: Conversion script

en:
Use this script to convert WFJ_optimaldataset_v6.smet to wfj.smet, the file that is used for the ESM-SnowMIP project. It also requires the file: WFJ_AirPressure_Data.zip

Use: bash create_wfj_dataset.sh > input/wfj.smet

mimetype: text/x-sh

en: This Weissfluhjoch dataset is a processed version of the Weissfluhjoch dataset version 6 from https://doi.org/10.16904/6. This dataset was specially created for the ESM-SnowMIP project. Here it is documented how this dataset has been created.

esm-snowmip

display_name: esm-snowmip

snow

display_name: snow

snow-depth

display_name: snow-depth

snow-models

display_name: snow-models

weissfluhjoch

display_name: weissfluhjoch

en: Weissfluhjoch dataset for ESM-SnowMIP


en: dry-snow-avalanche crack-propagation crack-speed weak-layer snow

en: manual profile taken next to the PSTs. Open the caaml-file using niviz.org

format: OCTET

en: Emodul parametrizations for snow. Some functions from this script are imported from the plotting scripts.

en: pickled version of the manual profile. read into python with pickle. E.g. given the density is used in plotting scripts.

en: pdf Version of the manual profile taken next to the PSTs

en: Jupyter script to load the netcdf files and reproduce Figure 4 from the related publication.

en: netCDF file of dispalcement and strain measurement of PST3 in full view perspective.

en: Jupyter script to load the netcdf files and reproduce Figure 3 from the related publication.

en: netCDF file of displacement and strain measurement of PST3 in closeup view.

en: Jupyter script to load the netcdf files and reproduce Figure 2 from the related publication.

en: netCDF file of dispalcement and strain measurement of PST2 in full view perspective.

media_type: image/tiff

en: reference frame used for Digital image correlation of the video of PST1

format: TIFF

en: netCDF file of dispalcement and strain measurement of PST1 in full view perspective.

en: netCDF file of dispalcement and strain measurement of PST2 in closeup view.

en:
This dataset contains the experimental results described in Bergfeld et al. (2025). It includes three Propagation Saw Test (PST) experiments, each approximately 9 m long, performed side-by-side on a 37° slope. For each PST, we provide the full field of view along the crack-propagation direction. For the second and third PSTs, we additionally provide close-up recordings focused on the weak layer where cracking occurred.
All data are supplied as netCDF files containing displacement and strain measurements derived from Digital Image Correlation (DIC) analysis. Metadata describing dimensions and units are stored directly within the netCDF files. We recommend using the xarray package in Python to read and work with these datasets.
All figures presented in Bergfeld et al. (2025) can be reproduced using the included Python scripts.
Information about the snowpack is provided in PDF, pickle, and CAAML file formats.

crack-propagation

display_name: crack-propagation

crack-speed

display_name: crack-speed

dry-snow-avalanche

display_name: dry-snow-avalanche

weak-layer

display_name: weak-layer

en: Sub-Rayleigh to supershear fracture transition in long Propagation Saw Tests


en: temperature permafrost ground borehole permos

en: PERMOS DATA POLICY

en: PERMOS Data Portal

en: Processed ground temperature measurements at the Fluelapass permafrost borehole A (FLU_0102) in canton Graubunden, Switzerland. The borehole is located at 2394 m asl on a moderate (26°) North-east slope (45°). The surface material is talus and borehole depth is 23 m. Thermistors used YSI 44006. Year of drilling 2002. This borehole is part of the Swiss Permafrost network, PERMOS (www.permos.ch). Contact phillips@slf.ch for details of processing applied.

borehole

display_name: borehole

ground

display_name: ground

permafrost

display_name: permafrost

permos

display_name: permos

temperature

display_name: temperature

educ

en: Education, culture and sport

envidat

en: EnviDat: the Environmental Data Portal

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

en: Processed permafrost borehole data (2394 m asl), Fluelapass A, Switzerland


restoring-grassland-multifunctionality

title_for_slug: restoring-grassland-multifunctionality

en: soil-biodiversity nematodes mineralization biodiversity grassland bacteria restoration fungi plants ecosystem-multifunctionality

format: XLS

en: Functional diversity above_belowground fauna

en: Please note that C.sto and Corg have been corrected.

en: Please note that EMF, MF.below, MF.abio and Soil.hetero have been corrected.

en:
Please cite this paper together with the citation for the datafile.

Resch, M. C., Schütz, M., Buchmann, N., Frey, B., Graf, U., van der Putten, W. H., Zimmermann, S., Risch, A. C. 2021. Evaluating long-term success in grassland restoration – an ecosystem multifunctionality approach. Ecological Applications 31, e02271.

 Study area

The study was conducted in the Canton of Zurich, Switzerland, in and around two nature reserves Eigental and Altläufe der Glatt (47°27’ to 47°29’ N, 8°37’ to 8°32’ E, 417 to 572 m a.s.l.). All studied grasslands were located with a radius of approximately 4 km. Average monthly temperatures range from 0.7 ± 2.0 °C (January) to 19.0 ± 1.5 °C (July), and monthly precipitation range from 60 ± 42 mm (January) to 118 ± 46 mm (July [maxima]; 1989-2017; MeteoSchweiz 2018). In our study, we focused on semi-dry and semi-wet oligo- to mesotrophic grasslands characterized by high plant species richness and groundwater fluctuations throughout the year (Delarze et al. 2015, see also Resch et al. 2019).

 Experimental design and sampling

A large-scale restoration experiment to expand and reconnect isolated remnants of species-rich grasslands was initiated in the nature reserve Eigental in 1990. Twenty hectares of adjacent intensive grasslands were chosen for restoration. In 1995, three restoration methods of increasing intervention intensities were implemented. The goal of all three methods was to lower the availability of soil nutrients and hence, facilitate ecosystem development towards the targeted nutrient-poor grasslands. These methods were: Harvest only (hay harvest twice a year), Topsoil (removal of the nutrient-rich topsoil), and Topsoil+Propagules (topsoil removal combined with the application of hay from target vegetation). Plant biomass harvest (once a year in late summer/early autumn) commenced in Topsoil and Topsoil+Propagules five years after the soils were removed and is still ongoing today. We measured restoration success by comparing the three restoration methods with intensively managed (Initial) and semi-natural grasslands (Target) 22 years after restoration. Initial grassland sites share the same agricultural history as the restored sites: mowing and subsequent fertilizing (manure) up to five times a year, as well as different tillage regimes (Resch et al. 2019). Target sites were the sites from which hay for seeding the Topsoil+Propagules sites was collected. Soil conditions (i.e., soil types, soil texture) were comparable to those found in the restored grasslands (Resch et al. 2019). Additionally, Target sites were selected to represent a variety of semi-natural grasslands, including semi-dry to semi-wet conditions. In Target grasslands, biomass is harvested once a year in late summer or early autumn. Eleven 5 m x 5 m (25 m2) plots were randomly established in each of the five treatments (in total 55 plots; for a detailed map see Neff et al. 2020). An additional 2 m x 2 m (4 m2) subplot was randomly established at least 2 m away from each 25 m2 plot for destructive sampling. Data sampling took place between June and September 2017.

Vegetation properties

All plant species were identified within the 25 m2 plots (nomenclature: Lauber and Wagner 1996) in mid-June 2017 (in total 250 species). Vegetation structure and plant biomass were assessed diagonally on a transect of 2 m x 10 cm within the 25 m2 plot in early July 2017. We measured the maximum and mean height of the vegetation at the start, middle and end of the transect and calculated the standard deviation of these measures to describe vegetation structural heterogeneity (Schuldt et al. 2019). Thereafter, biomass was clipped on the entire transect to 1 cm height, sorted into five functional groups (graminoids, forbs, legumes, litter, and woody species), dried at 60 °C for 48 h, and weighed (Meyer et al. 2015).

 Aboveground arthropods

Aboveground arthropods were sampled at two locations in each 25 m2 plot in early July 2017 (see also Neff et al. 2020). Briefly, two cylindrical baskets (50 cm diameter, 67 cm height; woven fabric) were thrown simultaneously from outside the plot into two opposite corners. A closable mosquito mesh sleeve was mounted to the top of the baskets and an integrated metal ring at the bottom was fixed to the ground with metal stakes to assure that insects could not escape. A suction sampler (Vortis, Burkhard Manufacturing Co. Ltd., Hertfordshire, England) was then inserted into one of the baskets through the opening of the sleeve and the plot was “vacuumed" twice for 105 seconds with a 30 seconds break. The collected animals were immediately transferred into 70% ethanol. Arthropods were sorted and assigned to 23 taxonomic groups. Holometabolic larvae were lumped into one category while hemimetabolic larvae were grouped separately from adults in the respective taxonomic rank. We used mean values of individuals per plot for total abundance. Aboveground arthropod richness was defined by the number of different taxa to lowest taxonomic level (in total 23 taxa). All taxa were assigned to one of five trophic levels: 1) primary producers, 2) primary consumers, 3) secondary consumers, 4) tertiary consumers, and 5) quaternary consumers.

 Belowground fauna

Sampling of all belowground fauna took place in mid-July 2017. Earthworms were sampled in two 30 cm x 30 cm x 20 cm soil monoliths at two opposite corners of the 25 m2 plot (opposite to aboveground arthropod sampling). The excavated soil monolith was broken by hand, all earthworms collected and immediately transferred in a 4% formaldehyde solution. Thereafter, earthworm individuals were identified to species level (in total 10 taxa; Christian and Zicsi 1999) and species assigned to three functional groups (Bouché 1977).
To assess soil arthropod communities, we randomly collected one undisturbed soil core (5 cm diameter, 12 cm depth) in each 4 m2 subplot with a slide hammer corer lined with a plastic sleeve (AMS Samplers, American Falls, Idaho, USA). Soil arthropods were extracted using Berlese-Tullgren funnels (3 mm mesh), starting the day of sampling and lasting 14 days. Individuals were stored in 70% ethanol. Soil arthropods were assigned to 41 taxonomic groups and 4 feeding types. Holometabolic and hemimetabolic larvae were treated as previously described for aboveground arthropods. Belowground arthropod richness refers to the 41 taxonomic groups.

For soil nematode sampling, we randomly collected eight soil cores of 2.2 cm diameter (Giddings Machine Company, Windsor, CO, USA) within each 4 m2 subplot to a depth of 12 cm. The eight cores were combined, gently homogenized, placed in coolers, kept at 4 °C and transported to the laboratory at NIOO in Wageningen (NL) within one week after collection. Free-living nematodes were extracted from 200 g of fresh soil using Oostenbrink elutriator (Oostenbrink 1960) and prepared for morphological identification and quantification as described by Resch et al. (2019). Nematodes were identified to family level (39 taxa) according to Bongers (1988), assigned to 17 functional groups, 5 feeding types and 5 colonizer-persister (C-P) classes (Yeates et al. 1993, Bongers 1990, Resch et al. 2019).

We randomly collected two more soil cores (2.2 cm diameter x 12 cm depth) within each 4 m2 subplot to determine soil microbial communities. Again, the soil cores were combined, homogenized, placed in coolers and transported to the laboratory at WSL in Birmensdorf (Switzerland) where the metagenomic DNA was extracted from 8 g sieved soil (2 mm) using the DNeasy PowerMax Soil Kit (Quiagen, Hilden, NRW, GER) according to the manufacturer`s instructions. PCR amplification of the V3-V4 region of the prokaryotic small-subunit (16S) and the ribosomal internal transcribed spacer region (ITS2) of eukaryotes was performed with 1 ng of template DNA utilizing PCR primers and conditions as previously described (Frey et al., 2016). PCRs were run in triplicates and pooled. The pooled amplicons were sent to the Genome Quebec Innovation Centre (Montreal, QC, Canada) for barcoding using the Fluidigm Access Array technology (Fluidigm) and paired-end sequencing on the Illumina MiSeq v3 platform (Illumina Inc., San Diego, CA, USA). Quality filtering, clustering into operational taxonomic units (OTUs) and taxonomic assignment were performed as described by Frey et al. (2016) and Adamczyk et al. (2019). We used a customised pipeline largely based on UPARSE (Edgar 2013) implemented in USEARCH v. 9.2 (Edgar 2010). After discarding singletons of dereplicated sequences, clustering into OTUs with 97% sequence similarity was performed (Edgar 2013). Quality-filtered reads were mapped on the filtered set of centroid sequences. Taxonomic classification of prokaryotic and fungal sequences was conducted querying against most recent versions of SILVA (v.132, Quast et al. 2013) and UNITE (v.8, Nilsson et al. 2018). Only taxonomic assignments with confidence rankings equal or higher than 0.8 were accepted (assignments below 0.8 set to unclassified). Prokaryotic OTUs assigned to mitochondria or chloroplasts as well as eukaryotic OTUs assigned other than fungi were removed prior to data analysis. In addition, prokaryotic and fungal datasets were filtered to discard singletons and doubletons. Thereafter, OTU abundance matrices were rarefied to the lowest number of sequences per community, to normalize the total number of reads and achieve parity between samples (Prokaryota: 29,843 reads; Fungi: 26,690 reads). Finally, prokaryotic and fungal observed richness (number of OTUs) were estimated (Prokaryota: 14,010 OTUs; Fungi: 5,813 OTUs). For prokaryotes, we distinguished five and for fungi six functional types based on lowest taxonomic resolution (Nguyen et al. 2016, Tedersoo et al. 2014). Belowground taxon richness was defined by the total number of earthworm, arthropod, nematode, fungi, and prokaryote taxa assigned to lowest taxonomic level. Finally, all belowground taxa were assigned to the same five trophic levels as the aboveground arthropods.

 Soil chemical and physical properties, soil nitrogen mineralization

We randomly collected three 5 cm diameter x 12 cm depth soil samples in each 4 m2 subplot with a slide hammer corer (AMS Samplers, American Falls, Idaho, USA), pooled them and then made two subsamples. One was field-fresh and stored at 3 °C until analysis, the other was dried for 48 h at 60 °C and passed through a 4 mm mesh. From the dried sample, we measured soil pH potentiometrically in 0.01 M CaCl2 (soil:solution ratio=1:2; 30 minutes equilibration time). Total and organic carbon content were measured on fine-ground samples (≤ 0.5 mm) by dry combustion using a CN analyzer NC 2500 (CE Instruments, Wigan, United Kingdom). Inorganic carbon of samples with a pH > 6.5 was removed with acid vapor prior to analysis of organic carbon (Walthert et al. 2010). We calculated total soil carbon (C) storage after correcting its content for soil depth, stone content and density of fine earth (see below). Exchangeable cations were determined on another 5 g dry soil sample with 50 mL unbuffered 1 M NH4Cl solution (soil:solution ratio=1:10, end-over-end shaker for 1.5 hours) and measured by an ICP-OES (Optima 7300 DV, Perkin-Elmer, Waltham, Massachusetts, USA). Thereafter, cation exchange capacity (CEC) was calculated as the sum of exchangeable cations and protons (and expressed as mmolc per 1 kg soil) and used to describe nutrient retention capacity in our plots. Concentrations of exchangeable protons were calculated as the difference between total and Al-induced exchangeable acidity as determined by the KCl-method (Thomas 1982).

Ammonium (NH4+) and nitrate (NO3−) were extracted from a 20 g fresh subsample with 80 mL 1M KCl for 1.5 hours on an end-over-end shaker and filtered through ashless folded filter paper (DF 5895 150, ALBET LabScience, Hahnemühle FineArt GmbH, Dassel, Germany). NH4+ concentrations were determined colorimetrically by automated flow injection analysis (FIAS 300, Perkin-Elmer, Waltham, Massachusetts, USA). NO3− concentrations were measured colorimetrically according to Norman and Stucki (1981). Potential soil net nitrogen (N) mineralization was assessed during an 8-week incubation period under controlled moisture (60% of field capacity), temperature (20 °C) and light conditions (dark) in the laboratory. We weighed duplicate samples of fresh soil equivalent to 8 g dry soil (24 h at 104 °C) into 50 mL Falcon tubes. Soil samples were extracted for NH4+ and NO3− at the beginning and after eight weeks as described above. Soil net N mineralization was calculated as the difference between the inorganic nitrogen (NH4+ and NO3−) before and after the incubation (Hart et al. 1994), corrected for the total incubation time and represented per day values expressed as mg N kg-1 soil d-1.

To assess soil physical properties, we randomly collected one undisturbed soil core per 4 m2 subplot (5 cm diameter, 12 cm depth) in a steel cylinder that fit into the slide hammer (AMS Samplers, American Falls, Idaho, USA). The cylinder was capped in the field to avoid disturbance. We then measured field capacity in the laboratory. For this purpose, the cylinder and soil therein were saturated in a water bath and drained on a sand/silt-bed with a suction corresponding to 60 cm hydrostatic head. The moist soil was dried at 105 °C to constant weight. Field capacity was calculated by dividing the mass of water by the total mass of wet soil contained at 60 cm hydrostatic head and used to describe water holding capacity. Thereafter, samples were passed through a 4 mm mesh. Fine-earth and skeleton fractions were weighed separately to assess bulk soil density (fine-earth plus skeleton), density of fine earth, and proportion of skeleton. Particle density was determined with the pycnometer method (Blake and Hartge 1986), and total porosity and proportion of fine pores were calculated (Danielson and Sutherland 1986). Clay, silt, and sand contents were quantified with the sediment method (Gee and Bauder 1986).

Surface and soil temperature (12 cm depth, water-resistant digital pocket thermometer; IP65, H-B Instrument, Trappe, Pennsylvania, USA) as well as volumetric soil moisture content (12 cm depth, time domain reflectometry; Field-Scout TDR 300, Spectrum Technologies, Aurora, Illinois, USA) were measured at five random locations within the 4 m2 subplots every month from June to September. We calculated the standard deviation of each temperature and moisture measure over four months to describe seasonal variations. Slope inclination was determined at plot-level via GPS measurements (GPS 1200, Leica Geosystem, Heerbrugg, Switzerland) and categorized into slope gradient classes according to FAO standards (1990). Thickness of the topsoil horizon (equivalent to Ah or Aa horizon) was determined at one soil monolith (30 x 30 x 30 cm3) per 4 m2 subplot in cm and rounded to next integer.

 References

Adamczyk, M., F. Hagedorn, S. Wipf, J. Donhauser, P. Vittoz, C. Rixen, A. Frossard, J. Theurillat, and B. Frey. 2019. The soil microbiome of GLORIA mountain summits in the Swiss Alps. Frontiers in Microbiology 10:1080-1101.

Blake, G.R., and K. H. Hartge. 1986. Particle Density. Pages 377-382 in A. Klute, editor. Methods of soil analysis: Part 1—Physical and mineralogical methods. Soil Science Society of America (SSSA) Inc., Madison.

Bongers, T. 1988. De nematoden van Nederland. Stichting Uitgeverij van de Koniklijke Nederlandse Natuurhistorische Verenigung (KNNV), Utrecht.

Bongers, T. 1990. The maturity index: an ecological measure of environmental disturbance based on nematode species composition. Oecologia 83:14-19.

Bouché, M. B. 1977. Strategies lombriciennes. Ecological Bulletins 25:122-132.

Christian, E., and A. Zicsi. 1999. Ein synoptischer Bestimmungsschlüssel der Regenwürmer Österreichs (Oligochaeta: Lumbricidae). Die Bodenkultur 50:121-131.

Danielson, R. E., and P. L. Sutherland. 1986. Porosity. Pages 443-461 in A. Klute, editor. Methods of soil analysis: Part 1—Physical and mineralogical methods. Soil Science Society of America (SSSA) Inc., Madison.

Delarze, R., Y. Gonseth, S. Eggenberg, and M. Vust. 2015. Lebensräume der Schweiz: Ökologie ‐ Gefährdung ‐ Kennarten, Ott Verlag, Bern.

Edgar, R. C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461.

Edgar, R. C. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10:996–998.

FAO. 1990. Guidelines for soil description, third ed. Land and Water Development Division at the Food and Agriculture Organization of the United Nations (FAO), Rome.

Frey, B., T. Rime, M. Phillips, B. Stierli, I. Hajdas, F. Widmer, and M. Hartmann. 2016. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiology Ecology 92:fiw018.

Gee, G.W., and J. W. Bauder. 1986. Particle-size analysis. Pages 383-411 in A. Klute, editor. Methods of soil analysis: Part 1—Physical and mineralogical methods. Soil Science Society of America (SSSA) Inc., Madison.

Hart, S. C, J. M. Stark, E. A. Davidson, and M. K. Firestone. 1994. Nitrogen mineralization, immobilization, and nitrification. Pages 985-1016 in R. W. Weaver, S. Angle, P. Bottomley, D. Bezdicek, S. Smith, A. Tabatabai, and A. Wollum, editors. Methods of soil analysis: Part 2—Microbiological and biochemical properties. Soil Science Society of America (SSSA) Inc., Madison.

Lauber, K., Wagner, G., 1996. Flora Helvetica. Flora der Schweiz. Haupt Verlag, Bern.

MeteoSchweiz, 2018. Klimabulletin Jahr 2017. MeteoSchweiz, Zürich.

Meyer, S. T., C. Koch, and W. W. Weisser. 2015. Towards a standardized rapid ecosystem function assessment (REFA). Trends in Ecology and Evolution 30:390-397.

Neff, F., M. C. Resch, A. Marty, J. Rolley, M. Schütz, A. C. Risch, and M. M. Gossner. 2020. Long-term restoration success of insect herbivore communities in semi-natural grasslands – a functional approach. Ecological Applications 0:e02133

Nguyen, N.H., Z. W. Song, S. T. Bates, S. Branco, L. Tedersoo, J. Menke, J. S. Schilling, and P. G. Kennedy. 2016. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology 20:241–248.

Nilsson, R. H., K.-H. Larsson, A. F. S. Taylor, J. Bengtsson-Palme, T. S. Jeppesen, D. Schigel, P. G. Kennedy, K. Picard, F. O. Glöckner, L. Tedersoo, I. Saar, U. Kõljalg, and K. Abarenkov. 2018. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research 47:259–264.

Norman, R. J., and J. W. Stucki. 1981. The Determination of Nitrate and Nitrite in Soil Extracts by Ultraviolet Spectrophotometry. Soil Science Society of America Journal 45:347-353.

Oostenbrink, M. 1960. Estimating nematode populations by some selected methods. Pages 81-101 in J. J. Sasser, and W. R. Jenkins, editors. Nematology. Univ. of North Carolina Press, Chapel Hill.

Quast, C., E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza, J. Peplies, and F. O. Glöckner. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41:590-596.

Resch, M. C., M. Schütz, U. Graf, R. Wagenaar, W.H. van der Putten, and A. C. Risch. 2019. Does topsoil removal in grassland restoration benefit both soil nematode and plant communities? Journal of Applied Ecology 56:1782-1793.

Schuldt, A., A. Ebeling, M. Kunz, M. Staab, C. Guimarães-Steinicke, D. Bachmann, N. Buchmann, W. Durka, A. Fichtner, F. Fornoff, W. Härdtle, L. R. Hertzog, A-N. Klein, C. Roscher, J. Schaller, von G. Oheimb, A. Weigelt, W. Weisser, C.Wirth, J. Zhang, H. Bruelheide, and N. Eisenhauer. 2019. Multiple plant diversity components drive consumer communities across ecosystems. Nature Communications 10:1460.

Tedersoo, L., M. Bahram, S. Põlme, U. Kõljalg, N. S. Yorou, R. Wijesundera, L. Villarreal Ruiz, A. M. Vasco-Palacios, P. Q. Thu, A. Suija, M. E. Smith, C. Sharp, E. Saluveer, A. Saitta, M. Rosas, T. Riit, D. Ratkowsky, K. Pritsch, K. Põldmaa, M. Piepenbring, C. Phosri, M. Peterson, K. Parts, K. Pärtel, E. Otsing, E. Nouhra, A. L. Njouonkou, R. H. Nilsson, L. N. Morgado, J. Mayor, T. W. May, L. Majuakim, D. J. Lodge, S. See Lee, K.-H. Larsson, P. Kohout, K. Hosaka, I. Hiiesalu, T. W. Henkel, H. Harend, L.-D. Guo, A. Greslebin, G. Grelet, J. Geml, G. Gates, W. Dunstan, C. Dunk, R. Frenkhan, L. Dearnaley, A. De Kesel, T. Dang, X. Chen, F. Buegger, F. Q. Brearley, G. Bonito, S. Anslan, S. Abell, and K. Abarenkov. 2014. Global diversity and geography of soil fungi. Science 346:1256688.

Thomas, G.W. 1982. Exchangeable cations. Pages 159-165 in A. L. Page, R. H. Miller, and D. R. Keeney, editors. Methods of Soil Analysis: Part 2—Chemical and microbiological properties. Soil Science Society of America (SSSA) Inc., Madison.

Walthert, L., U. Graf, A. Kammer, J. Luster, D. Pezzotta, S. Zimmermann, and F. Hagedorn. 2010. Determination of organic and inorganic carbon, δ13C, and nitrogen in soils containing carbonates after acid fumigation with HCl. Journal of Plant Nutrition and Soil Sciences 173:207-216.

Yeates, G. W., T. Bongers, R. G. M. de Goede, D. W. Freckman, and S. S. Georgieva. 1993. Feeding habits in soil nematode families and genera – an outline for soil ecologists. Journal of Nematology 25:315-331.

bacteria

display_name: bacteria

biodiversity

display_name: biodiversity

ecosystem-multifunctionality

display_name: ecosystem-multifunctionality

fungi

display_name: fungi

grassland

display_name: grassland

mineralization

display_name: mineralization

nematodes

display_name: nematodes

plants

display_name: plants

restoration

display_name: restoration

soil-biodiversity

display_name: soil-biodiversity

en: Restoring grassland multifunctionality


en: teleo marine fish-composition edna marseille mediterraneaen

en: Data access

en: Please use cyberduck to download for the moment

en:
Description: Fish environmental DNA data set collected in 2023 in the Calanques National Park
The eDNA samples were collected in 2023 in two locations (Moyades, M−FPA and “Impérial du large”, I-LPA), during the winter (January- February) season, with the sampling dates depending on the weather conditions. For the M−FPA, samples were collected between Moyades island and Riou island, while for the I-LPA, they were collected on the south side of the “Impérial du large” island. To account for the existing bathymetry, in the M−FPA the samples were taken at two sampling sites with depths of 20 and 40 m, while in the I-LPA they were taken at two sites with depths of 20 and 80 m.
At each site, in-situ filtration of seawater was performed using a double-head submersible pump (Subspace, Geneva, Switzerland; nominal flow of ca. 1 L/min) strapped to an underwater scooter with 2 VigiDNA 0.20 µm filtration capsules (SPYGEN, le Bourget du Lac, France), along with disposable sterile tubing. The samples were collected along two horizontal transects (up to 400 m in length) during each closed-circuit rebreather dive, enabling the filtration of a water volume of 15 L/filter per depth, as close as possible to the substrate. Two filter replicates were collected by two divers at each sampling site, except in two cases where bad weather conditions or logistical issues meant that only one replicate was sampled.
After the filtration, the remaining seawater was emptied from the capsule back on the boat and replaced by a 80 mL CL1 conservation buffer (SPYGEN, le Bourget du Lac, France). To prevent any contamination, a strict protocol was followed during the entire process, requiring disposable gloves and single-use filtration equipment. Finally, the samples were stored at room temperature. We followed a strict contamination control protocol in both field and laboratory stages. Each water sample processing included the use of disposable gloves and single-use filtration equipment to avoid any risk of contamination. Libraries were prepared with ligation using the MetaFast protocol (Fasteris).
Data content:
	* rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences.
	* taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata.
	* metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)

edna

display_name: edna

fish-composition

display_name: fish-composition

marine

display_name: marine

marseille

display_name: marseille

mediterraneaen

display_name: mediterraneaen

teleo

display_name: teleo

en: Environmental DNA Marine France Calanques 2023


maintainer: Gesa von Hirschheydt

en: sessile-species occupancy-model cryptogams detection-probability biodiversity swisslichens detectability monitoring observer-error lichens inter-observer-difference bayesian-inference

en: Repository containing the full data, code, README and workflow files.

en:
The available lichen data consists of detection/nondetection data (1/0) of 373 tree-inhabiting (*corticolous*) lichen species from 416 plots surveyed 1-2 times. The lichen data were originally collected for the purpose of the Red List of epiphytic lichen species in Switzerland ([Scheidegger *et al.* 2002](https://www.bafu.admin.ch/bafu/de/home/themen/biodiversitaet/publikationen-studien/publikationen/rote-liste-gefaehrdete-arten-baum-erdbewohnende-flechten.html)), but updated to recent nomenclature for the purpose of this study.
This repository contains all the supporting data and R code for the paper:
von Hirschheydt, G., Kéry, M., Ekman, S., Stofer, S., Dietrich, M., Keller, C., Scheidegger, C. (2024) **Occupancy model reveals limited detectability of lichens in a standardised large-scale monitoring**. *Journal of Vegetation Science*.
Results and figures presented in the manuscript should be reproducible (with small differences in the latter digits due to stochasticity of the MCMC sampler) with the provided data and code.
The downloadable `.zip` folder has the following structure:
* `0_data/`
* `1_code/`
* `2_output/`
* `lichen_detectability.Rproj`
* `README.txt`
* `workflow.html`
- `workflow.Rmd`

The main folder and the three subordinate folders each have their own `README*.txt` file. These describe each available file in detail and should be consulted prior to using the data or running any code. The file `lichen_detectability.Rproj` stores the information about the R project. The user can open the project by clicking/double-clicking on this file which will automatically define the repository as working directory for the R session. If the user does not use RStudio/Posit, they may have to set the working directory manually to the stored location in the R files. The files `workflow.*` guide the user through the analysis (`1_code/*.R`) in the correct order so that they can:
- bundle the cleaned data into a data list readable for JAGS
- fit the multi-species occupancy model to the data and store the output
- assess the goodness-of-fit of the model to the data
- conduct a prior sensitivity analysis with 2 additional sets of priors
- extract the summary statistics reported in the manuscript and supplementary materials
- generate the figures shown in the manuscript and supplementary materials

bayesian-inference

display_name: bayesian-inference

cryptogams

display_name: cryptogams

detectability

display_name: detectability

detection-probability

display_name: detection-probability

inter-observer-difference

display_name: inter-observer-difference

lichens

display_name: lichens

monitoring

display_name: monitoring

observer-error

display_name: observer-error

occupancy-model

display_name: occupancy-model

sessile-species

display_name: sessile-species

swisslichens

display_name: swisslichens

en: Repeated detection-nondetection data of corticolous lichens from a standardised monitoring across Switzerland


maintainer: Virginie Marques

en: marine fjord dna-metabarcoding fish biodiversity plankton environmental-dna

en: Code, data and figures

en: Here there are all the data and code to reproduce the figures and analysis presented in the paper, with a README.md file

en: Metabarcoding data

en: Raw metabarcoding data for both primers (teleo and 18S) and corresponding file to perform the demultiplexing and primer trimming

en:
This dataset contains the raw environmental DNA data associated with the publication *Environmental drivers of eukaryotic plankton and fish biodiversity in an Arctic fjord* in the journal Polar Biology (2023).

 Methods

**Sampling**
We sampled the Lilliehöök fjord on the west coast of Spitsbergen (Svalbard, Norway) over 3 days from 3 to 5 of August 2021. Samples were taken from the glacier front up to the fjord mouth of the Krossfjorden system, around 30 km long, after the Lilliehöök fjord merged with the mouth of Möller fjord. The fjord’s maximum depth has been recorded at 373 m (Svendsen et al. 2002) and has no sill at its entrance, thereby facilitating water exchange with the open ocean of the West Spitsbergen Current. We used a research vessel to sample 5 sites for a total of 15 samples, sampling 3 depths per site (3-m, chlorophyll a maximum and 85-m, unless sea floor was shallower). Shallow and intermediate samples between 3-m and 12-m represent ~35-L of water filtered in-situ using long tubing and a peristaltic pump, and all other deeper samples were taken from a total of 3 Niskin bottles (General Oceanics), representing 22-L of water sampled per sample. Water was filtered through a VigiDNA filtration capsule (SPYGEN) with a 0.20-µm pore size using an Athena peristaltic pump (Proactive Environmental Products, Bradenton, Florida) with a flow rate of ~1-L/min. Each sample was handled with single use tubing and gloves.

**Molecular**
To perform the amplification, we used two sets of primers: teleo (forward: ACACCGCCCGTCACTCT, reverse: CTTCCGGTACACTTACCATG; Valentini et al. 2016) and the universal eukaryotic 1389F/1510R primer pair, amplifying the V9-18S rDNA gene (Amaral-Zettler et al. 2009) (forward: TTGTACACACCGCCC, reverse: CCTTCYGCAGGTTCACCTAC).

 Data content:

+ Metabarcoding data: This zip file contains the 2 sequencing libraries filtered to only retain the samples used in the present study.
+ Code, data and figure: This zip file contains all data and code to reproduce the figures and the analysis in the study, with an associated README explaining the content of each folder.

 Additional informations
For more details, please see the Methods in the associated publication: DOI: 10.1007/s00300-023-03187-9.

biodiversity

display_name: biodiversity

dna-metabarcoding

display_name: dna-metabarcoding

environmental-dna

display_name: environmental-dna

fish

display_name: fish

fjord

display_name: fjord

plankton

display_name: plankton

educ

en: Education, culture and sport

envidat

en: EnviDat: the Environmental Data Portal

en: EnviDat is the WSL data portal providing unified and managed access to environmental monitoring and research data. The portal has the capability to host and publish data sets. Through the sharing of unique and high-value data sets worldwide, EnviDat fosters research and contributes to advancing environmental science.

en: Data: Environmental drivers of eukaryotic plankton and fish biodiversity in an Arctic fjord