Data Package Metadata View Summary

WARM experiment Soil Microbial Function, RMBL Colorado, 2021

General Information

Data Package:

Local Identifier:

edi.1575.2

Title:

WARM experiment Soil Microbial Function, RMBL Colorado, 2021

Alternate Identifier:

DOI PLACE HOLDER

Abstract:

We examined how abiotic (warming), and biotic (presence of dominant plant species) factors interact to affect soil microbial processes in montane meadow ecosystems at high and low elevations at the WaRM experimental sites near the Rocky Mountain Biological Laboratory in Colorado in the West Elk range of the southern Rocky Mountains in Colorado, USA, during the summer 2021 growing season. The low elevation site (low site) is at 2740 m elevation (38.715, -106.823) in an open meadow without tree cover, and the dominant plant species is a flowering forb, Wyethia amplexicaulis. The high elevation site (high site) (3460 m, 38.992, -107.067) is also described as open meadow with no tree cover and is dominated by Juncus drummondii, a monocot, grass-like herb. The low and high elevation sites have a mean summertime temperature of 14.9 and 10.9°C respectively, and a mean summertime precipitation of 143 and 151 mm

The WaRM experimental design is a 2 × 2 factorial warming × dominant plant species removal experiment deployed at the high elevation site and the low elevation site. Each of the four treatments are replicated 8 times, for total of 32 plots (each of which is 2 × 2 m) at each elevation with warming imposed via transparent hexagonal open-top chambers (OTCs), 1.5 m in diameter, in the center of each warming plot and the dominant plant species (listed above) removed via clipping at soil level within removal plots. Treatments at this site have been deployed each summer (June-August) since 2013.

We analyzed multiple soil microbial responses at three times throughout the growing season: pre-growing season [low site; approx. May 26, high site; approx. July 6], peak-growing season [low site; approx. June 23, high site; approx. July 21], and post-growing season [low site; approx. August 18, high site; approx. Sept 14]. We measured edaphic characteristics including volumetric soil water content. We measured soil microbial functions including soil respiration, microbial metabolic functional diversity, microbial biomass carbon and nitrogen, and extracellular enzyme potential activity.

Publication Date:

2024-02-15

For more information:
Visit:	DOI PLACE HOLDER

Time Period

Begin:

2021

End:

2021

People and Organizations
Contact:	McLaren, Jennie R (University of Texas at El Paso) [ email ]
Creator:	McLaren, Jennie R (University of Texas at El Paso, Associate Professor)
Creator:	Spinella, Sydne (University of Texas at El Paso)
Associate:	Classen, Aimee T (University of Michigan, Collaborator)
Associate:	Sanders, Nathan J (University of Michigan, Collaborator)

Data Entities
Data Table Name:	Spinella_DataForEDI
Description:	Biogeochemical and Microbial Function variables measured in a warming and plant removal experiment in montane meadow, Colorado

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1575/2/3ea06a49c7babce8c7ad631dcf6cdf4d
Name:	Spinella_DataForEDI
Description:	Biogeochemical and Microbial Function variables measured in a warming and plant removal experiment in montane meadow, Colorado
Number of Records:	192
Number of Columns:	25

Table Structure

Object Name:

Spinella_DataForEDI.csv

Size:

22959 byte

Authentication:

3eb6c57a08f57cff6383352f8b484c67 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Elevation

Sampling Timing

Plot Number

Warming Treatment

Removal Treatment

Volumetric Water Content

SoilTemp

AirTemp

SoilRespiration

NDVI

CLPPFunctionalDiversity

MBC

MBN

Extractable Organic Carbon

Extractable Total Nitrogen

Phosphatase

Phosphodiesterase

β-1,4-glucosidase

β-1,4-N-acetyl-glucosaminidase

β-D-1,4-cellobiosidase

β-1,4-Xylosidase

α-1,4-glucosidase

Leucine amino peptidase

Phenol Oxidase

Peroxidase

Column Name:

Elevation

Sampling

Plot

Warming

Removal

AvgVWC

SoilTemp

AirTemp

SoilRespiration

AvgNDVI

CLPPFunctionalDiversity

MBC

MBN

SoilEOC

SoilETN

Phosphatase

PhosD

B-gluc

NAG

Cello

B-xylo

a-gluc

LAP

Phenol

Perox

Definition:

There were 2 elevational sites in the WaRM experiment - low and high.

Soil samples were taken at 3 points throughout the summer growing season: pre-growing season after snow melt, peak-growing season at peak biomass growth, and post-growing season when >50% of biomass had senesced.

There were 32 plots at each elevational site that are randomly assigned to 1 of 4 treatments

Plots were either kept under ambient temperatures (A) or warmed with open-top chambers (W)

Plots were either kept under control plant composition treatment (C) or dominant plant species was removed (R).

Average of 4 measurements of volumetric water content (VWC) taken with soil moisture probe in situ

Temperature of soil in plots taken with thermometer

Temperature of the air in plots taken with thermometer

CO2 released from the soil with vegetation removed.

Average of 4 measurements of normalized difference vegetation index (NDVI) taken from each plot using a RapidScan

Community-level physiological profile measured using Biolog EcoPlates that analyze which forms of carbon can be broken down by microbial community in the soil sample. Functional diversity is calculated from this by dividing the number of substrates broken down out of 31 and multiplying by 100 to get a percentage.

Microbial Biomass Carbon (MBC) is a measure of the amount of carbon held within microbial cells in the soil samples, measured using a modified chloroform fumigation procedure

Microbial Biomass Nitrogen (MBN) is a measure of the amount of nitrogen held within microbial cells in the soil sample measured using a modified chloroform fumigation procedure

Extractable Organic Carbon (EOC) is a measure of the total extractable organic carbon in soil 0.5M K2SO4 extractions measured on a Shimadzu CN Analyzer

Extractable Total Nitrogen (ETN) is a measure of the total extractable nitrogen in soil 0.5M K2SO4 extractions measured on a Shimadzu CN Analyzer

Potential Phosphatase Activity in soil measured using measured using fluorescently tagged substrates in a microplate assay

Potential Phosphodiesterase Activity in soil measured using measured using fluorescently tagged substrates in a microplate assay

Potential β-1,4-glucosidase Activity in soil measured using measured using fluorescently tagged substrates in a microplate assay

Potential β-1,4-N-acetyl-glucosaminidase Activity in soil measured using measured using fluorescently tagged substrates in a microplate assay

Potential β-D-1,4-cellobiosidase Activity in soil measured using measured using fluorescently tagged substrates in a microplate assay

Potential β-1,4-Xylosidase Activity in soil measured using measured using fluorescently tagged substrates in a microplate assay

Potential α-1,4-glucosidase Activity in soil measured using measured using fluorescently tagged substrates in a microplate assay

Potential Leucine amino peptidase Activity in soil measured using measured using fluorescently tagged substrates in a microplate assay

Potential Phenol Oxidase Activity in soil measured using measured using L-Dopa substrates in a microplate assay

Potential Peroxidase Activity in soil measured using measured using L-Dopa substrates in a microplate assay

Storage Type:

string

float

Measurement Type:

nominal

ratio

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	High
Definition	High Elevation Site
Source

Code Definition

Code	Low
Definition	Low Elevation Site
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Peak
Definition	Peak growing season
Source

Code Definition

Code	Post
Definition	Post growing season
Source

Code Definition

Code	Pre
Definition	Pre growing season
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1
Definition	Plot number 1
Source

Code Definition

Code	2
Definition	Plot number 2
Source

Code Definition

Code	3
Definition	Plot number 3
Source

Code Definition

Code	4
Definition	Plot number 4
Source

Code Definition

Code	5
Definition	Plot number 5
Source

Code Definition

Code	6
Definition	Plot number 6
Source

Code Definition

Code	7
Definition	Plot number 7
Source

Code Definition

Code	8
Definition	Plot number 8
Source

Code Definition

Code	9
Definition	Plot number 9
Source

Code Definition

Code	10
Definition	Plot number 10
Source

Code Definition

Code	11
Definition	Plot number 11
Source

Code Definition

Code	12
Definition	Plot number 12
Source

Code Definition

Code	13
Definition	Plot number 13
Source

Code Definition

Code	14
Definition	Plot number 14
Source

Code Definition

Code	15
Definition	Plot number 15
Source

Code Definition

Code	16
Definition	Plot number 16
Source

Code Definition

Code	17
Definition	Plot number 17
Source

Code Definition

Code	18
Definition	Plot number 18
Source

Code Definition

Code	19
Definition	Plot number 19
Source

Code Definition

Code	20
Definition	Plot number 20
Source

Code Definition

Code	21
Definition	Plot number 21
Source

Code Definition

Code	22
Definition	Plot number 22
Source

Code Definition

Code	23
Definition	Plot number 23
Source

Code Definition

Code	24
Definition	Plot number 24
Source

Code Definition

Code	25
Definition	Plot number 25
Source

Code Definition

Code	26
Definition	Plot number 26
Source

Code Definition

Code	27
Definition	Plot number 27
Source

Code Definition

Code	28
Definition	Plot number 28
Source

Code Definition

Code	29
Definition	Plot number 29
Source

Code Definition

Code	30
Definition	Plot number 30
Source

Code Definition

Code	31
Definition	Plot number 31
Source

Code Definition

Code	32
Definition	Plot number 32
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	A
Definition	Ambient Temperature Treatment
Source

Code Definition

Code	W
Definition	Warmed Temperature Treatment
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	C
Definition	Control Plant Species Composition
Source

Code Definition

Code	R
Definition	Dominant Plant Species Removed
Source

Unit	percent
Type	real

Unit	degree
Type	real

Unit	degree
Type	real

Unit	micromolePerMeterSquaredPerSecond
Type	real

Unit	dimensionless
Type	real

Unit	percent
Type	real

Unit	microgramPerGram
Type	real

Unit	microgramPerGram
Type	real

Unit	microgramPerGram
Type	real

Unit	microgramPerGram
Type	real

Unit	microgramPerGramPerHour
Type	real

Unit	microgramPerGramPerHour
Type	real

Unit	microgramPerGramPerHour
Type	real

Unit	micromolePerGramPerHour
Type	real

Unit	microgramPerGramPerHour
Type	real

Unit	microgramPerGramPerHour
Type	real

Unit	microgramPerGramPerHour
Type	real

Unit	microgramPerGramPerHour
Type	real

Unit	nanomolePerGramPerHour
Type	real

Unit	nanomolePerGramPerHour
Type	real

Missing Value Code:

Code	NA
Expl	Plots were not available for measurement

Code	NA
Expl	Plots were not available for measurement

Code	NA
Expl	Plots were not available for measurement

Code	NA
Expl	Plots were not available for measurement

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)	Warming, Open top chamber, Elevation, Species removal, Extracellular Enzymes
LTER Controlled Vocabulary	soil respiration, microbial biomass

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:	A Hydrosense soil moisture probe was used to measure soil volumetric moisture (0- 10 cm) at each soil sampling timepoint
Instrument(s):	Hydrosense Soil Moisture Probe (Campbell Scientific, Logan UT, USA)

Description:	We measured the Normalized Difference Vegetation Index (NDVI) at each soil sampling using a RapidSCAN (Holland Scientific, Lincoln, Nebraska, USA) with 4 measurements taken from the corner of each plot and averaged together.
Instrument(s):	RapidSCAN (Holland Scientific, Lincoln, Nebraska, USA)

Description:	We measured soil respiration weekly using a LI-COR 6400XT with a 10 cm diameter soil respiration chamber (LI-COR Biosciences, Lincoln, Nebraska, USA) with above-ground living plant material removed.
Instrument(s):	LI-COR 6400XT (LI-COR Biosciences, Lincoln, Nebraska, USA)

Description:

Potential microbial metabolism was analyzed on a community level using a Biolog EcoPlate assay. Briefly, 4 g of soil was suspended with 36 mL of potassium phosphate buffer and a dilution of this suspension added into 96 well ECO plates. Plates were incubated before being analyzed. Functional diversity in CLPPs between soil samples was calculated by observing the richness (number of positive tests after background correction) of sample responses to all 31 carbon sources

Description:

We quantified MBC and MBN using a modification of the chloroform fumigation method. Two sets of soil extracts, one fumigated with chloroform and one not, were analyzed for extractable organic carbon (EOC) and extractable total nitrogen (ETN) using a Shimadzu CN analyzer (Shimadzu Scientific Instruments Inc., Columbia, Maryland, USA). Microbial flushes representing MBC and MBN were calculated as the difference between EOC and ETN in fumigated and non-fumigated extracts.

Instrument(s):

Shimadzu CN analyzer (Shimadzu Scientific Instruments Inc., Columbia, Maryland, USA)

Description:

Exoenzyme activity on collected soils was measured via microplate assays. Hydrolytic enzymes were measured using fluorescently tagged substrates and oxidative enzymes (phenol oxidase (Phenol) and peroxidase (Perox)) using L-3, 4-dihydroxyphenylalanine substrate in a slurry with soil and sodium acetate buffer adjusted to the site-specific soil pH (6.3 for low site, 4.4 for high site).

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:

Jennie R McLaren

Organization:

University of Texas at El Paso

Position:

Associate Professor

Email Address:

jrmclaren@utep.edu

Id:

https://orcid.org/0000-0003-2004-4783

Individual:	Sydne Spinella
Organization:	University of Texas at El Paso

Contacts:

Individual:

Jennie R McLaren

Organization:

University of Texas at El Paso

Email Address:

jrmclaren@utep.edu

Id:

https://orcid.org/0000-0003-2004-4783

Associated Parties:

Individual:	Aimee T Classen
Organization:	University of Michigan
Id:	https://orcid.org/0000-0002-6741-3470
Role:	Collaborator

Individual:	Nathan J Sanders
Organization:	University of Michigan
Id:	https://orcid.org/0000-0001-6220-6731
Role:	Collaborator

Temporal, Geographic and Taxonomic Coverage

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

Time Period

Begin:

2021

End:

2021

Sampling Site:

Description:

Low elevation site

Site Coordinates:

Longitude (degree):	-106.823	Latitude (degree):	38.715
Altitude (meter):	2740.0

Sampling Site:

Description:

High elevation site

Site Coordinates:

Longitude (degree):	-107.067	Latitude (degree):	38.992
Altitude (meter):	3460.0

Project

Parent Project Information:

Title:

Warming and dominant species removal effects on soil microbial function in an alpine meadow

Personnel:

Individual:	Jennie R McLaren
Organization:	University of Texas at El Paso
Id:	https://orcid.org/0000-0003-2004-4783
Role:	Data Owner

Individual:	Sydne Spinella
Organization:	University of Texas at El Paso
Role:	Data Co-Owner

Additional Award Information:

Funder:	University of Texas at El Paso
Title:	Warming effects on soil microbial function

Additional Award Information:

Funder:	Rocky Mountain BIological Laboratory
Title:	Warming effects on soil microbial function

Maintenance

Maintenance:

Description:

Data was collected by S. Spinella

Data was QA'd by S.Spinella and JR McLaren

Data will be updated by JR McLaren as necessary

Frequency:

asNeeded

Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'emlEditor'
        |     |        \___attribute 'app' = 'ezEML'
        |     |        \___attribute 'release' = '2024.02.07'
        |     |___text '\n      '
        |___text '\n   '

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

Data Package Metadata View Summary

WARM experiment Soil Microbial Function, RMBL Colorado, 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

WARM experiment Soil Microbial Function, RMBL Colorado, 2021

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Data Table

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+/- Keywords

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

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Methods and Protocols

People and Organizations

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Maintenance

Additional Metadata