Data Package Metadata View Summary

NEON distributed initial soil characterization dataset subsetted for statistical analysis of organic carbon and extractable metals in Hall and Thompson (2021)

General Information

Data Package:
Local Identifier:	edi.476.1
Title:	NEON distributed initial soil characterization dataset subsetted for statistical analysis of organic carbon and extractable metals in Hall and Thompson (2021)
Alternate Identifier:	DOI PLACE HOLDER
Abstract:	We compiled National Ecological Observatory Network (NEON) datasets related to the initial distributed soil sampling effort and subsetted them (removed samples with missing values for certain variables, and several samples with extreme values) for use in statistical analyses to describe relationships between soil organic carbon (SOC) and metals measured in several soil chemical extractions. The NEON provisional data products we used were DP1.10047.001 and DP1.10008.001, which were subsequently combined by NEON as a single data product DP1.10047.001, “Soil physical and chemical properties, distributed initial characterization”. These datasets were used for the analyses reported in a manuscript by Hall and Thompson (2021) in the Soil Science Society of America Journal.
Publication Date:	2021-09-27

Time Period

Begin:

2020-12-01

End:

2021-08-01

People and Organizations
Contact:	Hall, Steven J (Iowa State University) [ email ]
Creator:	Hall, Steven J (Iowa State University)
Creator:	Thompson, Aaron (University of Georgia)

Data Entities
Data Table Name:	NEON dataset for SOC and metal analysis
Description:	NEON dataset for SOC and metal analysis

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/476/1/4a74579113c0e664e125ca132cfd1395
Name:	NEON dataset for SOC and metal analysis
Description:	NEON dataset for SOC and metal analysis
Number of Records:	2540
Number of Columns:	53

Table Structure

Object Name:

NEON_soil_chem_for_stats_plots.csv

Size:

969696 bytes

Authentication:

3ea20cf2e09e973f3b261cf53a60f835 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

plotID

horizonID

pitID

domainID

siteID

horizonName

biogeoTopDepth

biogeoCenterDepth

biogeoBottomDepth

soilOrder

soilSuborder

soilGreatGroup

soilSubgroup

soilFamily

soilSeries

Andic

Spodic

soilSamplingMethod

decimalLatitude

decimalLongitude

elevation

sandTotal

siltTotal

clayTotal

silt_plus_clay

carbonTot

nitrogenTot

ctonRatio

estimatedOC

phH2o

phCacl2

alOxalate

feOxalate

siOxalate

alOxalate_mol_kg

feOxalate_mol_kg

siOxalate_mol_kg

alCitDithionate_mol_kg

feCitDithionate_mol_kg

siCitDithionate_mol_kg

siOxalate_mol_kg_minus_siCitDithionate_mol_kg

alOxalate_mol_kg_minus_alCitDithionate_mol_kg

caNh4d

mgNh4d

caNh4d_plus_mgNh4d

alCitDithionate

feCitDithionate

feCitDithionate_minus_feOxalate

NLCD_veg

grouped_NLCD_veg

map_minus_pet

mat

map

Definition:

Plot identifier (NEON site code_XXXX)

An identifier for the soil horizon

pitID

Unique identifier of the NEON domain

Four letter NEON site code

Soil horizon name

Top depth of the biogeochemistry sample

Depth of the center of the biogeochemistry sample

Bottom depth of the biogeochemistry sample

Soil taxonomy at the order level

Soil taxonomy at the suborder level

Soil taxonomy at the great group level

Soil taxonomy at the subgroup level

Soil taxonomy at the family level

Soil taxonomy at the series level

Sample was collected from an Andisol or a soil designated with andic properties

Sample was collected from a Spodosol or a soil designated with spodic properties

The methodology used for collecting soil at a plot (pit or core)

The geographic latitude (in decimal degrees, WGS84) of the geographic center of the reference area

The geographic longitude (in decimal degrees, WGS84) of the geographic center of the reference area

Elevation (in meters) above sea level

Total sand (0.047-2 mm) content on a weight basis of the <2 mm fraction

Total silt (0.002-0.047 mm) content on a weight basis of the <2 mm fraction

Total clay (<0.002 mm) content on a weight basis of the <2 mm fraction

Total silt plus clay content on a weight basis of the <2 mm fraction

Total carbon concentration of the <2 mm fraction

Total nitrogen concentration of the <2 mm fraction

Ratio of total Carbon to total Nitrogen of the <2 mm fraction

Estimated organic carbon concentration of the <2 mm fraction

pH of the <2 mm fraction in water

pH of the <2 mm fraction in CaCl2

Total soil Al as estimated by the ammonium oxalate extraction method, reported as weight percent on the <2 mm fraction

Total soil noncrystalline iron as measured by the ammonium oxalate extraction method, reported as weight percent on the <2mm fraction

Total soil silica content as measured by the ammonium oxalate extraction method, reported as a weight percent on a <2 mm base

Oxalate-extractable Al, reported as moles per kg on a <2 mm basis

Oxalate-extractable Fe, reported as moles per kg on a <2 mm basis

Oxalate-extractable Si, reported as moles per kg on a <2 mm basis

Citrate-dithionite extractable Al, reported as moles per kg on a <2 mm basis

Citrate-dithionite extractable Fe, reported as moles per kg on a <2 mm basis

Citrate-dithionite extractable Si, reported as moles per kg on a <2 mm basis

The difference between oxalate-extractable Si and citrate-dithionite-extractable Si, reported as moles per kg on a <2 mm basis

The difference between oxalate-extractable Al and citrate-dithionite-extractable Al, reported as moles per kg on a <2 mm basis

Ammonium acetate extractable calcium from the <2 mm fraction

Ammonium acetate extractable magnesium from the <2 mm fraction

The sum of ammonium acetate extractable calcium and magnesium from the <2 mm fraction

Dithionite citrate extractable aluminum content, reported as weight percent on the <2mm fraction

Dithionite citrate extractable iron, a general measure of total pedogenic iron, reported as weight percent on the <2mm fraction

The difference between Fe measured in citrate-dithionite and oxalate extraction, reported as weight percent on the <2mm fraction

Vegetation type according to the NLCD classification

Binned NLCD vegetation type

Mean annual precipitation minus potential evapotranspiration (WorldClim)

Mean annual temperature (WorldClim)

Mean annual precipitation (WorldClim)

Storage Type:

string

float

string

float

string

float

Measurement Type:

nominal

ratio

nominal

ratio

nominal

ratio

Measurement Values Domain:

Definition

Plot identifier (NEON site code_XXXX)

Definition

An identifier for the soil horizon

Definition

pitID

Definition

Unique identifier of the NEON domain

Definition

Four letter NEON site code

Definition

Soil horizon name

Definition

Top depth of the biogeochemistry sample

Definition

Depth of the center of the biogeochemistry sample

Definition

Bottom depth of the biogeochemistry sample

Definition

Soil taxonomy at the order level

Definition

Soil taxonomy at the suborder level

Definition

Soil taxonomy at the great group level

Definition

Soil taxonomy at the subgroup level

Definition

Soil taxonomy at the family level

Definition

Soil taxonomy at the series level

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	no
Source

Code Definition

Code	1
Definition	yes
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	no
Source

Code Definition

Code	1
Definition	yes
Source

Definition

The methodology used for collecting soil at a plot (pit or core)

Unit	degree
Type	real
Min	17.951583
Max	71.316715

Unit	degree
Type	real
Min	-156.650984
Max	-66.824633

Unit	meter
Type	real
Min	2.1
Max	3500.3

Unit	percent
Type	real
Min	1.2
Max	98.9

Unit	percent
Type	real
Min	0.3
Max	80.7

Unit	percent
Type	real
Min	0
Max	84.7

Unit	percent
Type	real
Min	1.1
Max	98.8

Unit	gramPerKilogram
Type	real
Min	0.5
Max	206

Unit	gramPerKilogram
Type	real
Min	0
Max	16.2

Definition

Ratio of total Carbon to total Nitrogen of the <2 mm fraction

Unit	gramPerKilogram
Type	natural
Min	1
Max	193

Unit	dimensionless
Type	real
Min	3.1
Max	10

Unit	dimensionless
Type	real
Min	2.6
Max	9.5

Unit	percent
Type	real
Min	0.001
Max	2.87

Unit	percent
Type	real
Min	0.001
Max	2.95

Unit	percent
Type	real
Min	0.001
Max	1.44

Unit	molePerKilogram
Type	real
Min	0
Max	1.063

Unit	molePerKilogram
Type	real
Min	0
Max	0.528

Unit	molePerKilogram
Type	real
Min	0
Max	0.513

Unit	molePerKilogram
Type	real
Min	0
Max	0.751

Unit	molePerKilogram
Type	real
Min	0
Max	1.488

Unit	molePerKilogram
Type	real
Min	0
Max	0.179

Unit	molePerKilogram
Type	real
Min	-0.112
Max	0.419

Unit	molePerKilogram
Type	real
Min	-0.337
Max	0.726

Unit	centimolePerKilogram
Type	real
Min	0
Max	143.7

Unit	centimolePerKilogram
Type	real
Min	0
Max	34.8

Unit	centimolePerKilogram
Type	real
Min	0
Max	155.1

Unit	percent
Type	real
Min	0
Max	2.03

Unit	percent
Type	real
Min	0
Max	8.31

Unit	percent
Type	real
Min	0
Max	7.98

Definition

Vegetation type according to the NLCD classification

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1
Definition	forest
Source

Code Definition

Code	2
Definition	grassland/shrubland
Source

Code Definition

Code	3
Definition	cropland
Source

Code Definition

Code	4
Definition	wetland
Source

Unit	millimeter
Type	integer
Min	-2084
Max	1382

Unit	celsius
Type	real
Min	-12
Max	26.1

Unit	millimeter
Type	natural
Min	106
Max	2449

Missing Value Code:

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Code	NA
Expl	missing data

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
(No thesaurus)	Macrosystems Biology, NEON, Soil, Soil Organic Matter, Biogeochemistry, Soil Horizon, Soil Carbon, Oxalate, Citrate Dithionite, Poorly Crystalline Mineral, Iron, Aluminum, Silicon, Soil Extraction, Metal

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:

We downloaded the provisional NEON datasets referenced below on December 12, 2020. These samples were collected and analyzed by USDA NRCS staff in collaboration with NEON, and further information about methodology of sample collection and analysis is available in the original datasets cited below. Inspection of the data revealed that metal concentrations reported for the citrate-dithionite extraction had been rounded to a single decimal place, so these values were not readily comparable with the ammonium oxalate extraction. Therefore, we obtained the raw metal concentrations from the USDA NRCS staff who conducted the original analyses (USDA NRCS, personal communication, April 15, 2021); the new citrate-dithionite data reported here were rounded to two decimal places for comparison to the ammonium oxalate extraction data.

Multiple data files from these downloaded NEON datasets (spc_particlesize.csv, spc_perhorizon.csv, spc_perplot.csv, spc_biogeochem.csv) were merged in R (version 3.6.3) to create a single file, using “horizonID” or “pitID” as the common variable for each sample, and columns with extraneous information not immediately relevant to our analyses were removed. Climate data from the WorldClim database (Fick and Hijmans 2017) were added for each sample as described in a previous related publication (Yu et al., 2021). We also added vegetation type data obtained from the R package “geoNEON” (NEON 2020), following the terminology of the National Land Cover Database; these were binned into four broader classes (forest, grassland/shrubland, wetland, cropland) for subsequent use as model predictors, following Yu et al. (2021).

After combining these datasets into a single file, we trimmed the dataset and created additional predictor variables using the following criteria. Horizons classified as organic by NRCS staff (O horizon) were removed, along with any samples with SOC concentrations > 200 mg/g (consistent with the definition of an O horizon). Samples with undetectable SOC were also removed. For use as predictor variables, concentrations of silt- and clay-sized particles were summed, as were concentrations of exchangeable calcium and magnesium. The mass concentrations of Al + 0.5Fe in the oxalate extraction were summed for use as a predictor, as this has traditionally been used as an approximation for the molar sum of poorly-crystalline Fe and Al. Crystalline iron (Fe) phases were estimated as the difference between citrate-dithionite and oxalate extractable Fe; two samples with large negative values (< -1%) were removed, and remaining negative values were set to zero.

We include two versions of this dataset, each used for different purposes. The dataset “NEON_distributed_soil_dataset_for_gamm.csv” was used for statistical analyses (generalized additive mixed models, GAMMs) to test relationships between SOC and extractable metals. Here, 9 samples with oxalate-extractable Al and Fe > 3% were excluded, as they had very high leverage. We also removed any samples with missing values for any predictor used in the statistical analyses: oxalate-extractable Al, Fe or Si, citrate-dithionite-extractable Al or Fe, or silt+clay. This left 2540 soil horizon samples for GAMM analysis. The second dataset “NEON_soil_chem_for_metals_plots.csv” was used to examine pairwise relationships between metals in the citrate-dithionite and ammonium oxalate extractions. No samples were removed from this dataset, for a total of 2,596 samples. We conducted preliminary analyses where we assessed the of ratios of metals (iron, aluminum, silicon) in the oxalate and citrate-dithionite extractions, so zero values for any metal were replaced with a small positive number (0.001%; smallest reported positive values in the dataset were 0.01%), and mass concentrations were converted to mole concentrations for bivariate analyses. Andisols or Spodosols or soils with andic designators in Family or Subgroup names in the USDA soil taxonomy were denoted with a binary categorical variable for analysis purposes (i.e., comparison of all soils, soils with andic/spodic properties, and soils without andic/spodic properties).

<emphasis role="strong">References</emphasis>

Fick, S. E., & Hijmans, R. J. (2017). WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology, 37(12), 4302–4315. https://doi.org/10.1002/joc.5086

NEON (National Ecological Observatory Network). Soil physical properties, distributed initial characterization (DP1.10047.001). https://data.neonscience.org (accessed December 12, 2020)

NEON (National Ecological Observatory Network). Soil chemical properties, distributed initial characterization (DP1.10008.001). https://data.neonscience.org (accessed December 12, 2020)

National Ecological Observatory Network (2020). geoNEON: Geolocation Data Access for NEON Data. R package version 1.0.0.9100.

Yu, W, Weintraub, S.R., and S.J. Hall. 2021. <link xlink:href="https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020GB006781">Climatic and geochemical controls on soil carbon at the continental scale: interactions and thresholds</link>. Global Biogeochemical Cycles 35: e2020GB006781.

Description:

This method step describes provenance-based metadata

This provenance metadata does not contain entity specific information.

Data Source

Soil physical and chemical properties, distributed initial characterization (DP1.10047.001)

People and Organizations

Publishers:

Organization:

Environmental Data Initiative

Email Address:

info@environmentaldatainitiative.org

Web Address:

https://environmentaldatainitiative.org

Creators:

Individual:

Steven J Hall

Organization:

Iowa State University

Email Address:

stevenjh@iastate.edu

Id:

https://orcid.org/0000-0002-7841-2019

Individual:

Aaron Thompson

Organization:

University of Georgia

Email Address:

aaront@uga.edu

Id:

https://orcid.org/0000-0001-6301-7377

Contacts:

Individual:

Steven J Hall

Organization:

Iowa State University

Email Address:

stevenjh@iastate.edu

Id:

https://orcid.org/0000-0002-7841-2019

Temporal, Geographic and Taxonomic Coverage

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

Time Period

Begin:

2020-12-01

End:

2021-08-01

Geographic Region:

Description:

North America

Bounding Coordinates:

Northern:	69	Southern:	18
Western:	-150	Eastern:	-65

Project

Parent Project Information:

Title:

Collaborative Research: MSB-ECA: Resolving controls on lignin decomposition at the continental scale to reconcile classical and modern paradigms of soil organic matter

Personnel:

Individual:

Steven J Hall

Organization:

Iowa State University

Email Address:

stevenjh@iastate.edu

Id:

https://orcid.org/0000-0002-7841-2019

Role:

Principal Investigator

Funding:

NSF DEB 1802745

Maintenance

Maintenance:

Description:	completed
Frequency:

Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'unitList'
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'centimolePerKilogram'
        |     |     |     |  \___attribute 'multiplierToSI' = '100'
        |     |     |     |  \___attribute 'name' = 'centimolePerKilogram'
        |     |     |     |  \___attribute 'parentSI' = 'molePerKilogram'
        |     |     |     |  \___attribute 'unitType' = 'amountOfSubstanceWeight'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text '1/100 of a mole per kilogram'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'gramPerKilogram'
        |     |     |     |  \___attribute 'multiplierToSI' = '1/1000'
        |     |     |     |  \___attribute 'name' = 'gramPerKilogram'
        |     |     |     |  \___attribute 'parentSI' = 'gramPerGram'
        |     |     |     |  \___attribute 'unitType' = 'massPerMass'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'gram per kilogram'
        |     |     |     |___text '\n        '
        |     |     |___text '\n      '
        |     |___text '\n    '
        |___text '\n  '

Copyright 2024 Environmental Data Initiative. This material is based upon work supported by the National Science Foundation under grants #2223103 and #2223104. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Please contact us with questions, comments, or for technical assistance regarding this web site or the Environmental Data Initiative. Please read our privacy policy to know what information we collect about you and to understand your privacy rights.

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

Data Package Metadata View Summary

NEON distributed initial soil characterization dataset subsetted for statistical analysis of organic carbon and extractable metals in Hall and Thompson (2021)

Data Entities

Data Table

Data Package Usage Rights

Keywords

Methods and Protocols

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

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Parent Project Information:

Maintenance

Additional Metadata

Recently Added

Recently Updated

Data Package Metadata View Summary

NEON distributed initial soil characterization dataset subsetted for statistical analysis of organic carbon and extractable metals in Hall and Thompson (2021)

+/- Data Entities

Data Table

+/- Data Package Usage Rights

+/- Keywords

+/- Methods and Protocols

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

+/- People and Organizations

+/- Temporal, Geographic and Taxonomic Coverage

+/- Project

Parent Project Information:

+/- Maintenance

+/- Additional Metadata

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance

Additional Metadata