Data Package Metadata   View Summary

Ectomycorrhizal fungal effects on soil carbon storage, root litter decomposition, and fungal necromass decomposition

General Information
Data Package:
Local Identifier:knb-lter-cdr.731.1
Title:Ectomycorrhizal fungal effects on soil carbon storage, root litter decomposition, and fungal necromass decomposition
Alternate Identifier:knb-lter-cdr.715.2
Alternate Identifier:DOI PLACE HOLDER
Abstract:
This project investigates the impacts of ectomycorrhizal-saprotrophic fungal interactions on soil C storage and the decomposition of root litter and fungal necromass. Specifically, we conducted a field experiment wherein the ectomycorrhizal:saprotrophic fungal ratio was reduced via experimental trenching (with control plots left untrenched). From these plots we then measured bulk soil C stocks, particulate organic matter C stocks, mineral associated organic matter C stocks, and the decomposition of root litter and fungal necromass. The Cedar Creek Ecosystem Science Reserve (CCESR) experiment name is e309 "The effects of mycelial morphology and mycorrhizal type on fungal necromass decomposition."
Short Name:aike120
Publication Date:2023-08-03
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
2020
End:
2020

People and Organizations
Contact:Bahauddin, Dan (Cedar Creek LTER, Information Manager) [  email ]
Creator:DeLancey, Lang C (University of Minnesota, Graduate Student)
Creator:Maillard, Francois (Lund University, Postdoctoral researcher)
Creator:Hobbie, Sarah E (University of Minnesota, Distinguished McKnight University Professor)
Creator:Kennedy, Peter G (University of Minnesota, Professor)

Data Entities
Data Table Name:
soil_data
Description:
Ectomyccorhizal fungal effects on soil carbon storage
Data Table Name:
decomp_data
Description:
Ectomyccorhizal fungal effects on belowground tissue decomposition
Other Name:
EcolLet2023_DeLancey_Code
Description:
This folder is intended to be accessed through the "EcolLet2023_DeLancey_Code.Rproj" project file. To do so, please download the two relevant data files housed in the same Environmental Data Initiative repository and place them in this folder. Once this is completed, there are two R scripts contained within this project to reproduce the analyses for the manuscript. "Soil Code.R" reproduces analyses for the first 3 subsections of the results section. These analyses pertain to root stocks, soil fungal abundances, soil carbon (C) stocks, and relating changes in C stocks to changes in fungal abundances. "Belowground Decomp.R" reproduces analyses for the final subsection of the results section. These analyses pertain to the decomposition of roots and fungal necromass. Separate scripts to reproduce figures are provided and are labelled by figure. Please note that minor, aesthetic modifications to figures were made in an image editing program (Inkscape) to add statistical information (ANOVA results, pairwise comparisons), add panel demarcations (e.g a), b) etc.), or shift legend positions. All data called in these R scripts is available through the environmental data initiative and will be contained in the folder with this code.
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-cdr/731/1/b9f4fd4ddb5e75de87bd20d4441b245f
Name:soil_data
Description:Ectomyccorhizal fungal effects on soil carbon storage
Number of Records:96
Number of Columns:40

Table Structure
Object Name:soil_data.csv
Size:29677 byte
Authentication:8125136912f8ac5622f2fd5ff86b5c5f Calculated By MD5
Text Format:
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Record Delimiter:\r\n
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Table Column Descriptions
 YEARSampleNumSampleCodeSitePlotUniquePlotTreatmentDepth_IncrementDepthTopcm_DepthBulk_pctCBulk_pctNBulk_CNBulkDensityCstock_m2Cstock_m3RootMass_Fine_DepthRootMass_Total_DepthEMF_abundSap_abundEctoSap_ratioqPCR_abundLF_pctCLF_pctNLF_CNSHP_pctCSHP_pctNSHP_CNSC_pctCSC_pctNSC_CNPOM_CNLF_kgC.m2SHP_kgC.m2SC_kgC.m2POM_kgC.m2LF_kgC.m3SHP_kgC.m3SC_kgC.m3POM_kgC.m3
Column Name:YEAR  
SampleNum  
SampleCode  
Site  
Plot  
UniquePlot  
Treatment  
Depth_Increment  
DepthTop  
cm_Depth  
Bulk_pctC  
Bulk_pctN  
Bulk_CN  
BulkDensity  
Cstock_m2  
Cstock_m3  
RootMass_Fine_Depth  
RootMass_Total_Depth  
EMF_abund  
Sap_abund  
EctoSap_ratio  
qPCR_abund  
LF_pctC  
LF_pctN  
LF_CN  
SHP_pctC  
SHP_pctN  
SHP_CN  
SC_pctC  
SC_pctN  
SC_CN  
POM_CN  
LF_kgC.m2  
SHP_kgC.m2  
SC_kgC.m2  
POM_kgC.m2  
LF_kgC.m3  
SHP_kgC.m3  
SC_kgC.m3  
POM_kgC.m3  
Definition:Year of collectionUnique identifier for each sampleUnique code for each sample following the form site_plot_treatment_depthSite, either Pine 1 or Pine 2Plot numberCombindation of Site and blockWhether subplot was trenched or notDepth increment of soil sampledTop of depth incrementTotal Height of Core AreaBulk soil percent carbonBulk soil percent nitrogenBulk soil carbon-to-nitrogen ratioBulk soil bulk densityCarbon stock expressed on an areal basis Carbon stock expressed on a volumetric basisFine root (<2 mm) standing stock mass on a volumetric basisTotal root standing stock mass on a volumetric basissum or rarefied sequence read counts assigned to the ectomycorrhizal guildsum or rarefied sequence read counts assigned to the saprotrophic guildRatio of Ectomycorrhizal-to-saprotrophic abundancesLog10 of Abundance of fungi as determined by real-time quantitative PCR (qPCR)Light fraction (LF) percent carbonLight fraction (LF) percent nitrogenLight fraction (LF) carbon-to-nitrogen ratioSand and heavy particulate organic matter (SHP) pecent carbonSand and heavy particulate organic matter (SHP) percent nitrogenMineral-associated organic matter (silt and clay fraction; SC) carbon-to-nitrogen ratioMineral-associated organic matter (silt and clay fraction; SC) percent carbonMineral-associated organic matter (silt and clay fraction; SC) percent nitrogenMineral-associated organic matter (silt and clay fraction; SC) carbon-to-nitrogen ratioParticulate Organic Matter carbon-to-nitrogen ratioLight fraction (LF) carbon stock on a areal basisSand and heavy particulate organic matter (SHP) carbon stock on a areal basisMineral-associated organic matter (silt and clay fraction; SC) carbon stock on a areal basisParticulate organic matter carbon stock on a areal basis. This is a sum of LF and SHP stocksLight fraction (LF) carbon stock on a volumetric basisand and heavy particulate organic matter (SHP) carbon stock on a volumetric basisMineral-associated organic matter (silt and clay fraction; SC) carbon stock on a volumetric basisParticulate organic matter carbon stock on a volumetric basis. This is a sum of LF and SHP stocks
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Measurement Type:dateTimenominalnominalnominalnominalnominalnominalnominalrationominalratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratio
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Accuracy Report:                                                                                
Accuracy Assessment:                                                                                
Coverage:                                                                                
Methods:                                                                                

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-cdr/731/1/4722298d604f156d2b6fb3dbcf77bb65
Name:decomp_data
Description:Ectomyccorhizal fungal effects on belowground tissue decomposition
Number of Records:192
Number of Columns:22

Table Structure
Object Name:decomp_data.csv
Size:32228 byte
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Table Column Descriptions
 YEARSampleNumSitePlotUniquePlotPlotCodeTreatmentTypeStartEndIncubationMonthsGenusLatinGenusBinomialTreeMycoFungalGuildTreePhylogenyFungalMelanininitial_pctCinitial_pctNinitial_CNprop_mass_remain
Column Name:YEAR  
SampleNum  
Site  
Plot  
UniquePlot  
PlotCode  
Treatment  
Type  
Start  
End  
IncubationMonths  
Genus  
LatinGenus  
Binomial  
TreeMyco  
FungalGuild  
TreePhylogeny  
FungalMelanin  
initial_pctC  
initial_pctN  
initial_CN  
prop_mass_remain  
Definition:YearUnique indentifier for each sampleSite, either Pine 1 or Pine 2Plot numberCombination of Site and blockA combination of Site, Plot, and TreatmentWhether subplot was trenched or notTissue typeIncubation start month and yearIncubation end month and yearDuration of in-soil incubation in monthsCommon name of genusLatin genus nameLatin binomial nameMycorrhizal Type of Tree SpeciesFungal Functional GuildTree phylogenyRelative melanin content of fungal necromassInitial percent carbon of tissueInitial percent nitrogen of tissueInitial carbon-to-nitrogen ratio of tissueProportion mass remaining at time of harvest
Storage Type:dateTime  
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Measurement Type:dateTimenominalnominalnominalnominalnominalnominalnominalnominalnominalrationominalnominalnominalnominalnominalnominalnominalratioratioratioratio
Measurement Values Domain:
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Precision
Definitiontext
Definitiontext
Definitiontext
Definitiontext
Definitiontext
Allowed Values and Definitions
Enumerated Domain 
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CodeControl
DefinitionUntrenched
Source
Code Definition
CodeTrenched
DefinitionTrenched
Source
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Unitpercent
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CodeNA
Explnot applicable
Accuracy Report:                                            
Accuracy Assessment:                                            
Coverage:                                            
Methods:                                            

Non-Categorized Data Resource

Name:EcolLet2023_DeLancey_Code
Entity Type:zip
Description:This folder is intended to be accessed through the "EcolLet2023_DeLancey_Code.Rproj" project file. To do so, please download the two relevant data files housed in the same Environmental Data Initiative repository and place them in this folder. Once this is completed, there are two R scripts contained within this project to reproduce the analyses for the manuscript. "Soil Code.R" reproduces analyses for the first 3 subsections of the results section. These analyses pertain to root stocks, soil fungal abundances, soil carbon (C) stocks, and relating changes in C stocks to changes in fungal abundances. "Belowground Decomp.R" reproduces analyses for the final subsection of the results section. These analyses pertain to the decomposition of roots and fungal necromass. Separate scripts to reproduce figures are provided and are labelled by figure. Please note that minor, aesthetic modifications to figures were made in an image editing program (Inkscape) to add statistical information (ANOVA results, pairwise comparisons), add panel demarcations (e.g a), b) etc.), or shift legend positions. All data called in these R scripts is available through the environmental data initiative and will be contained in the folder with this code.
Physical Structure Description:
Object Name:EcolLet2023_DeLancey_Code.zip
Size:3438380 byte
Authentication:58d7ea1b2fad795acf0a22b41e7437dd Calculated By MD5
Externally Defined Format:
Format Name:zip
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-cdr/731/1/49b0d4d823df18d9eef1d944ee9071ee

Data Package Usage Rights

This data package is released to the "public domain" under Creative Commons CC0 1.0 "No Rights Reserved" (see: https://creativecommons.org/publicdomain/zero/1.0/). It is considered professional etiquette to provide attribution of the original work if this data package is shared in whole or by individual components. A generic citation is provided for this data package on the website https://portal.edirepository.org (herein "website") in the summary metadata page. Communication (and collaboration) with the creators of this data package is recommended to prevent duplicate research or publication. This data package (and its components) is made available "as is" and with no warranty of accuracy or fitness for use. The creators of this data package and the website shall not be liable for any damages resulting from misinterpretation or misuse of the data package or its components. Periodic updates of this data package may be available from the website. Thank you.

Intellectual Rights for Cedar Creek LTER data

This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.

  • This is a human-readable summary of (and not a substitute for) the license.
  • You are free to copy and redistribute the material in any medium or format
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  • The licensor cannot revoke these freedoms as long as you follow the license terms.
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  • Notice - You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation.
  • Notice - No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material.

Keywords

By Thesaurus:
LTER Controlled Vocabularydecomposition, fungi, microbial activity, soil carbon, root decomposition, forests
(No thesaurus)Cedar Creek, CDR

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:
Site Description This experiment was conducted at the University of Minnesota Cedar Creek Ecosystem Science Reserve in central Minnesota, USA, a National Science Foundation Long Term Ecological Research site (45.42577N, 093.20852W). Specifically, this study was conducted in two second-growth Pinus strobus (eastern white pine) stands located 1.2 km apart, hereafter referred to as sites 1 and 2. Suppression of Pinus strobus needle litter decomposition in the litter layer has been observed previously at site 1 (Fernandez et al., 2020). Soils at both sites are poorly developed, very sandy (~89%) Udipsamments (Grigal et al., 1974). Eight replicate blocks were established at each of these sites in June 2018. Each block consisted of two side-by-side plots (1 m2), one of which had root and EMF connections severed by passing a handsaw down to 30 cm from the top of the mineral soil every two weeks of the full growing season (hereafter trenching). The other plot was left untrenched as a control.
Description:
Soil Sampling and SOM Fractionation To assess how trenching impacted soil C, soils were sampled at three different depths (0-5 cm, 5-10 cm, 10-20 cm from the litter-mineral soil interface) in July 2020. Two replicate soil cores were collected from each plot using a 5.2 cm diameter split hammer corer, divided into depth increments and homogenized, then transported on ice to the lab for further processing. Soils were then sieved to 2 mm to isolate standing root stock and air-dried. Bulk density of each depth increment was calculated by taking cores in a 5 x 4 grid (20 total cores) spanning each site to capture spatial variation. Bulk density sampling was conducted outside of plots to minimize damage to plots, as it was assumed that trenching would not affect bulk density in these coarse soils. To assess the effects of trenching on distinct SOM pools, we used a density- and size-fractionation procedure to separate POM and MAOM(Soong and Cotrufo, 2015, Lavallee et al., 2019). Briefly, light-POM was less dense than 1.85 g cm-3 (as determined in sodium metatungstate), heavy-POM was denser than 1.85 g cm-3 and larger than 53 µm (by wet sieving), and MAOM was denser than 1.85 g cm-3 and smaller than 53 µm. Detailed fractionation methods are provided in the supplementary materials. Each fraction (as well as bulk soil) was analyzed for C and N content by dry combustion (Costech 4010 Elemental Analyzer, Valencia, CA, USA). For simplicity of analyses, light- and heavy-POM fractions were summed to yield a single POM fraction (Lavallee et al., 2019). To account for the differing sampling depth increments (0-5, 5-10, 10-20 cm) when analyzing across depths, C stocks are expressed on a volumetric basis (kg C m-3). When pooled across the full 20 cm sampling depth, however, a more standard area-basis stock is used (kg C m-2).
Description:
Fungal Guild Abundances To assess the effects of trenching on fungal guild abundance, aliquots were sterilely sampled from soil cores at each depth described above, transported to the lab on ice, and frozen at -80°C before extraction. DNA was extracted from 250 mg soil samples using Qiagen DNEasy Power Soil Pro kits. Soil fungal communities were analyzed using high throughput sequencing (HTS), as in Maillard et al. (in press). We present analysis on the guild level (i.e. ectomycorrhizal and saprotrophic) based on sums of rarefied sequence read counts from those guilds (hereafter referred to as guild abundances). These two guilds dominated our samples with EMF and saprotrophic fungi accounting for 46.9% and 33.4% of total fungal read counts, respectively. To quantify total fungal abundances in the same samples, we used real-time quantitative PCR (hereafter qPCR), expressed as log10 of numbers of fungal 18S copies per gram of dry soil. More detailed descriptions of molecular methods, including guild categorization, are provided in the supplementary materials.
Description:
Belowground Tissue Decomposition To assess the effects of trenching on belowground tissue decomposition, roots and fungal mycelia (hereafter necromass) were incubated in mesh bags(initial mass 150 mg in 53 µm-mesh bags)in mineral soil at a depth of 2.5 cm from the litter-mineral soil interface in trenched and control plots. Fine root (less than 2 mm in diameter) litter of four tree species was collected and pooled from stands within 1 km of study sites, then dried at 60°C for 3 days before being deployed in monospecific bags. Root litter species were selected to represent locally common tree species with differing tissue chemistry (e.g C:N), phylogeny (gymnosperm vs. angiosperm), and mycorrhizal association (arbuscular vs. EMF), which have previously been implicated in determining root decomposition dynamics (See et al., 2019, Table 1). Root litter bags were incubated for 12 months (August 2019-August 2020). Fungal necromass of two species was grown in liquid culture (1/2 concentration potato dextrose broth) for 30 days for Mortierella elongata, and 60 days for Meliniomyces bicolor to achieve similar masses. After sufficient mass was generated, cultures were rinsed with DI water and dried at 26°C before being ground with a mortar and pestle and passed through a 250 µm sieve. Fungal necromass was incubated in the field for 3 months (August-October 2019). Necromass species were selected to vary in C and N content, as well as melanin content, which has been shown to be a major control over necromass decomposition (Fernandez et al., 2018, See et al., 2020, Table 1), and both species are naturally present in these sites (data not shown). Initial C and N concentrations of roots and necromass were determined by dry combustion. Both root and necromass species are referred to by genus name.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@edirepository.org
Web Address:
https://edirepository.org
Id:https://ror.org/0330j0z60
Creators:
Individual: Lang C DeLancey
Organization:University of Minnesota
Position:Graduate Student
Email Address:
lang.delancey@gmail.com
Id:https://orcid.org/0000-0001-5605-5834
Individual: Francois Maillard
Organization:Lund University
Position:Postdoctoral researcher
Email Address:
francois.maillard@biol.lu.se
Id:https://orcid.org/0000-0002-2144-5629
Individual: Sarah E Hobbie
Organization:University of Minnesota
Position:Distinguished McKnight University Professor
Email Address:
shobbie@umn.edu
Id:https://orcid.org/0000-0001-5159-031X
Individual: Peter G Kennedy
Organization:University of Minnesota
Position:Professor
Email Address:
kennedyp@umn.edu
Id:https://orcid.org/0000-0003-2615-3892
Contacts:
Individual: Dan Bahauddin
Organization:Cedar Creek LTER
Position:Information Manager
Address:
Ecology Evolution and Behaviour Dept. University Of Minnesota,
100 Ecology Building,
Saint Paul, MN 55108 USA
Email Address:
webmaster@cedarcreek.umn.edu
Id:https://orcid.org/0000-0003-1190-2926
Id:https://ror.org/03a976s92
Metadata Providers:
Individual: Lang C DeLancey
Organization:University of Minnesota
Position:Postdoctoral researcher
Email Address:
lang.delancey@gmail.com
Id:https://orcid.org/0000-0001-5605-5834

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2020
End:
2020
Geographic Region:
Description:The Cedar Creek Ecosystem Science Reserve is located in Anoka and Isanti counties, approximately 30 miles north of Saint Paul, MN. CCNHA lies at the boundary between prairie and forest. It is a mosaic of uplands dominated by oak savanna, prairie, hardwood forest, pine forests,and abandoned agricultural fields and of lowlands comprised of ash and cedar swamps, acid bogs, marshes, and sedge meadows. Large tracts of the pre-agricultural ecosystems of the region are preserved within its boundaries, as is a successional chronosequence of more than 80 old fields of known history.
Bounding Coordinates:
Northern:  45.44138Southern:  45.384865
Western:  -93.22445Eastern:  -93.16289

Project

Parent Project Information:

Title:The effects of mycelial morphology and mycorrhizal type on fungal necromass decomposition.
Personnel:
Individual: Peter G Kennedy
Organization:University of Minnesota
Position:Professor
Email Address:
kennedyp@umn.edu
Id:https://orcid.org/0000-0003-2615-3892
Role:Principle Investigator
Additional Award Information:
Funder:National Science Foundation
Number:DEB-1831944
Title:LTER: Multi-decadal responses of prairie, savanna, and forest ecosystems to interacting environmental changes: insights from experiments, observations, and models
Additional Award Information:
Funder:National Science Foudation
Number:DEB-1234162
Title:LTER: Biodiversity, Multiple Drivers of Environmental Change and Ecosystem Functioning at the Prairie Forest Border

Maintenance

Maintenance:
Description:This data is not expected to be continued, and the data package will only be updated to correct errors or update metadata.
Frequency:
Other Metadata

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        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'CopiesPerGram'
        |     |     |     |  \___attribute 'name' = 'CopiesPerGram'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n      '
        |     |___text '\n    '
        |___text '\n  '

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'emlEditor'
        |     |        \___attribute 'app' = 'ezEML'
        |     |        \___attribute 'release' = '2023.07.06'
        |     |___text '\n    '
        |___text '\n  '

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

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