Data Package Metadata   View Summary

Physiological responses of biological soil crusts in the Chihuahuan desert

General Information
Data Package:
Local Identifier:knb-lter-jrn.210549002.2
Title:Physiological responses of biological soil crusts in the Chihuahuan desert
Alternate Identifier:DOI PLACE HOLDER
Abstract:

This dataset contains photosynthetic light response and carbon fixation data from biological soil crusts collected at four locations in the Chihuahuan Desert. This study aims to 1) assess the carbon fixation capacity of biocrust types under varying incubation times; 2) assess biocrust nitrogen fixation capacity; 3) understand microbial community composition as well as biomass differences within these biocrust types; and 4) identify how geographic location and soil properties can explain differences seen in carbon fixation and microbial diversity. In order to characterize the physiology of biocrust types at a range of Chihuahuan Desert sites, intact, replicate samples of five soil crust types were collected from each of 4 sites in southern New Mexico, USA: the Jornada Experimental Range (near T-West), the A-Mountain BLM site, the Volcanic BLM site, and White Sands Missile Range. Data and sample collection occurred between May and July of 2020, and the soil crust types of interest were light cyanobacterial, dark cyanobacterial, Peltula lichen, Clavascidium lichen, and moss crusts (n=5 samples for each site & type). After collection, crust subsamples were sequenced, targeting the 16S rRNA gene region for bacteria (see EDI dataset knb-lter-jrn.210549001 and linked data at NCBI), and then subjected to an incubation and photosynthetic response measurements. The intact crusts were incubated under low light, and C fixation was then observed under 12-point light regime in a LI-6400XT photosynthesis analyzer leaf chamber after incubation periods of 30min, 2hr, 6hr, 12hr, and 24hr (5 reps for each condition). The resulting light response curves were used to calculate photosynthetic information in R for the purpose of comparing biocrust type, site, and time response differences and upscale carbon flux values to landscape scale. This data set includes the light response curve values and photosynthetic data calculated from these curves. This data set also includes raw LICOR output files compiled into four Excel workbooks that data was extracted from. This study is complete.

Short Name:soil crust physiology (hoellrich)
Publication Date:2021-10-20
Language:English

Time Period
Begin:
2020-05-01
End:
2020-07-31

People and Organizations
Contact:Jornada Basin LTER Information Manager (Jornada Basin LTER) [  email ]
Creator:Hoellrich, Mikaela (New Mexico State University)
Creator:Pietrasiak, Nicole (New Mexico State University)
Associate:Dominguez, Andrew (New Mexico State University, associate)
Associate:De Ley, Paul (New Mexico State University, associate)

Data Entities
Data Table Name:
Biological soil crust C fixation data
Description:
Light response curves and carbon fixation data collected during incubations of biological soil crusts collected at 4 sites in the Chihuahuan desert.
Data Table Name:
Raw licor output variables
Description:
Description and units of raw LiCor data outputs
Other Name:
Raw licor data AMT
Description:
Raw LiCor 6400 data from AMT
Other Name:
Raw licor data JER
Description:
Raw LiCor 6400 data from JER
Other Name:
Raw licor data VOL
Description:
Raw LiCor 6400 data from VOL
Other Name:
Raw licor data WHS
Description:
Raw LiCor 6400 data from WHS
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549002/2/0472480128d83d9e64de6b4b081596c0
Name:Biological soil crust C fixation data
Description:Light response curves and carbon fixation data collected during incubations of biological soil crusts collected at 4 sites in the Chihuahuan desert.
Number of Records:499
Number of Columns:24

Table Structure
Object Name:JRN549002_Cfix_and_lightresponse.csv
Size:121651 byte
Authentication:0c6a0864bee0102c8f81fe3f339f9e53 Calculated By MD5
Text Format:
Number of Header Lines:1
Number of Foot Lines:0
Record Delimiter:\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 Sampling siteBiocrust typeTimeRepThicknessWaterPercentWaterCfixRespirationNetQuantumYieldSaturatingPPFDPAR0PAR25PAR50PAR100PAR150PAR300PAR500PAR750PAR1000PAR1250PAR1600PAR2000
Column Name:Site  
Type  
Time  
Rep  
Thickness  
Water  
PercentWater  
Cfix  
Respiration  
Net  
QuantumYield  
SaturatingPPFD  
PAR0  
PAR25  
PAR50  
PAR100  
PAR150  
PAR300  
PAR500  
PAR750  
PAR1000  
PAR1250  
PAR1600  
PAR2000  
Definition:Sampling site codeCrust type codeTime into incubation in hoursReplicate numberThickness of the biocrust samplesWater content of samplePercent water content in sampleDifference between highest and lowest curve pointsMinimal value of carbon fixationHighest point from raw dataInitial slope of line indicating the efficiency of light absorption - Umol CO2 fixed/umol photons absorbedPhotosynthetic photon flux density at which carbon fixation no longer increases with more light intensityRaw data net CO2 fixation at 0 umol m-2 sec-1 lightRaw data net CO2 fixation at 25 umol m-2 sec-1 lightRaw data net CO2 fixation at 50 umol m-2 sec-1 lightRaw data net CO2 fixation at 100 umol m-2 sec-1 lightRaw data net CO2 fixation at 150 umol m-2 sec-1 lightRaw data net CO2 fixation at 300 umol m-2 sec-1 lightRaw data net CO2 fixation at 500 umol m-2 sec-1 lightRaw data net CO2 fixation at 750 umol m-2 sec-1 lightRaw data net CO2 fixation at 1000 umol m-2 sec-1 lightRaw data net CO2 fixation at 1250 umol m-2 sec-1 lightRaw data net CO2 fixation at 1600 umol m-2 sec-1 lightRaw data net CO2 fixation at 2000 umol m-2 sec-1 light
Storage Type:string  
string  
string  
integer  
float  
float  
float  
float  
float  
float  
float  
integer  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
Measurement Type:nominalnominalnominalintervalratioratioratioratioratioratioratiointervalratioratioratioratioratioratioratioratioratioratioratioratio
Measurement Values Domain:
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeAMT
DefinitionA Mountain BLM site
Source
Code Definition
CodeJER
DefinitionJornada Experimental Range site (near T-WEST)
Source
Code Definition
CodeVOL
DefinitionVolcanic BLM site
Source
Code Definition
CodeWHS
DefinitionWhite Sands Missile Range site
Source
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeCVL
DefinitionClavascidium lichen crust
Source
Code Definition
CodeDA
Definitiondark algal crust
Source
Code Definition
CodeLA
Definitionlight algal crust
Source
Code Definition
CodeMO
DefinitionMoss crust
Source
Code Definition
CodePTL
DefinitionPeltula lichen crust
Source
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codetwelve
DefinitionTwelve hours into incubation
Source
Code Definition
Codetwo
DefinitionTwo hours into incubation
Source
Code Definition
Codetwenty-four
Definition24 hours into incubation
Source
Code Definition
Codesix
DefinitionSix hours into incubation
Source
Code Definition
Codehalf
DefinitionHalf an hour into incubation
Source
Unitnumber
Typeinteger
Unitmillimeter
Typereal
Unitmilliliter
Typereal
Unitpercent
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
Unitdimensionless
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typeinteger
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
UnitmicromolePerMeterSquaredPerSecond
Typereal
Missing Value Code:          
CodeNA
ExplMissing value - data not collected or otherwise unavailable
CodeNA
ExplMissing value - data not collected or otherwise unavailable
     
CodeNA
ExplMissing value - data not collected or otherwise unavailable
                         
Accuracy Report:                                                
Accuracy Assessment:                                                
Coverage:                                                
Methods:                                                

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549002/2/2c5ee35295be5e75fb32501488e0d927
Name:Raw licor output variables
Description:Description and units of raw LiCor data outputs
Number of Records:55
Number of Columns:3

Table Structure
Object Name:RawLicor_variable_key.csv
Size:1915 byte
Authentication:e677f6f21e4588a69a456db3d27983f9 Calculated By MD5
Text Format:
Number of Header Lines:1
Number of Foot Lines:0
Record Delimiter:\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 Column namePAR2000PAR2000
Column Name:Column_name  
Column_description  
Unit_codes_or_date_format  
Definition:Column or variable name in LiCor raw output fileDescription of column or variableMeasurement units, categorical code, or dateTime format of column
Storage Type:string  
string  
string  
Measurement Type:nominalnominalnominal
Measurement Values Domain:
Definitionany text
Definitionany text
Definitionany text
Missing Value Code:    
CodeNA
ExplMissing value - data not collected or otherwise unavailable
Accuracy Report:      
Accuracy Assessment:      
Coverage:      
Methods:      

Non-Categorized Data Resource

Name:Raw licor data AMT
Entity Type:otherEntity
Description:Raw LiCor 6400 data from AMT
Physical Structure Description:
Object Name:AMTRawLicorFix.xlsx
Size:2038273 byte
Authentication:4a5f06b5911024ddc6506adfbe0b9b34 Calculated By MD5
Externally Defined Format:
Format Name:MS-Excel
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549002/2/1b4be31e227e13bfbc673dc4758b3e83

Non-Categorized Data Resource

Name:Raw licor data JER
Entity Type:otherEntity
Description:Raw LiCor 6400 data from JER
Physical Structure Description:
Object Name:JERRawLicorFix.xlsx
Size:2005107 byte
Authentication:977bb0088c793898e1dfbebe7ca84264 Calculated By MD5
Externally Defined Format:
Format Name:MS-Excel
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549002/2/b02e45682253ed23f5c8e3f6a7ad66ae

Non-Categorized Data Resource

Name:Raw licor data VOL
Entity Type:otherEntity
Description:Raw LiCor 6400 data from VOL
Physical Structure Description:
Object Name:VOLRawLicorFix.xlsx
Size:2011313 byte
Authentication:f6f0f16662f679cfacbfec64a0c1db83 Calculated By MD5
Externally Defined Format:
Format Name:MS-Excel
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549002/2/3d8ed63ddc0a32d0df069ad72915c80a

Non-Categorized Data Resource

Name:Raw licor data WHS
Entity Type:otherEntity
Description:Raw LiCor 6400 data from WHS
Physical Structure Description:
Object Name:WHSRawLicorFix.xlsx
Size:1997037 byte
Authentication:be57d2dc982517571db7964193b1d0d1 Calculated By MD5
Externally Defined Format:
Format Name:MS-Excel
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549002/2/eccc5511d4d08b77bd954860f2dec78c

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:
LTER Core Research AreasPopulations
LTER Controlled Vocabulary v1algae, bacterial abundance, carbon assimilation, community dynamics, deserts, genomics, incubation, photosynthesis, soil, soil samples, species abundance, species diversity, transects
none16S sequencing, biological, biotic crusts, carbon fixation, cryptobiotic crusts, cyanobacteria, incubation, light response, photosynthesis, relative abundance, soil crusts
Jornada Basin LTER dataset keywordsNCBI linked, non-core
Jornada Basin project namesstudy 549
Jornada Basin place namesT-WEST

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:

Experimental and sampling design

Biological soil crusts, and related environmental data and samples, were collected at four sites in the Chihuahuan Desert with varying vegetation and soils. At each of the four sites in the study, 2 intersecting 30m transects were laid out in an X shape crossing at the 15m mark. From these transects, intact, replicate samples of 5 types of biological soil crusts were collected. Collections occurred between May and July of 2020. Soil metagenomic analyses were performed using subsamples of each crust, and the data from these analyses are stored at the NCBI Sequence Read Archive under NCBI BioProject #PRJNA748083. Further information about these analyses can also be found in the related EDI dataset knb-lter-jrn.210549001. After being returned to the lab, the intact crust samples were subsequently incubated and observed using the following methods.

Incubations and photosynthetic measurements

Intact crust samples were wet to field capacity, cut into 1.6x1.7cm square and incubated under light incubator (~90 mmol/m2/s) for an allotted period of time before photosynthetic measurements were collected at 30min, 2hr, 6hr, 12hr, or 24hr., Samples were rewetted every 6 hours and/or 30min before ending the incubation. During each set of photosynthetic measurements, each sample was weighed and placed into LI-6400XT photosynthesis analyzer leaf chamber and subjected to a 12 point light regime (PAR: 0, 25, 50, 100, 150, 300, 500, 750, 1000, 1250, 1600, 2000 umol/s). After the incubations ended, samples were dried at 105˚C for 48hr and reweighed for dry weight. Subsequent light response curve points were pulled from raw licro data file. Photosynthetic data was extracted from each curve: Maximum carbon fixation, Net fixation rate, Respiration rate, Quantum Yield, and Saturating light intensity. Samples were processed July-August 2020 in the apartment of Mikaela Hoellrich, due to COVID-19 lab restrictions.

Notes

NA values in the Water and Percent Water columns indicates issue in data collection leading to removal of value. NA in LightCompensation indicates the response curve was an atypical shape and did not meet the criterion for the value. A 2000 in SaturatingPPFD indicates that there was no saturation. Sample data missing for Sample (JER DA two rep5), it was probably accidentally deleted at some point after data collection.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@environmentaldatainitiative.org
Web Address:
https://environmentaldatainitiative.org
Id:https://ror.org/0330j0z60
Creators:
Individual: Mikaela Hoellrich
Organization:New Mexico State University
Address:
,
Las Cruces, NM 88003-8003 U.S.A.
Individual: Nicole Pietrasiak
Organization:New Mexico State University
Address:
,
Las Cruces, NM 88003-8003 U.S.A.
Id:https://orcid.org/0000-0003-4636-8006
Contacts:
Organization:Jornada Basin LTER
Position:Jornada Basin LTER Information Manager
Address:
P.O. Box 30003, MSC 3JER New Mexico State University,
Las Cruces, NM 88003-8003 USA
Phone:
575-646-1739
Email Address:
jornada.data@nmsu.edu
Web Address:
https://lter.jornada.nmsu.edu/information-management/
Associated Parties:
Individual: Andrew Dominguez
Organization:New Mexico State University
Role:associate
Individual: Paul De Ley
Organization:New Mexico State University
Role:associate
Metadata Providers:
Organization:Jornada Basin LTER
Address:
P.O. Box 30003; MSC 3JER New Mexico State University,
Las Cruces, NM 88003-8003 USA
Web Address:
https://lter.jornada.nmsu.edu

Temporal, Geographic and Taxonomic Coverage

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

Time Period
Begin:
2020-05-01
End:
2020-07-31
Geographic Region:
Description:T-West crust sampling (549): Study 549 T-West crust samples: Near T- West, tarbush dominated site
Bounding Coordinates:
Northern:  32.511184Southern:  32.511065
Western:  -106.741358Eastern:  -106.741125
Geographic Region:
Description:A Mountain crust sampling (549): Study 549 A Mountain crust samples: Across the road from A Mountain, creosote dominated
Bounding Coordinates:
Northern:  32.300009Southern:  32.300001
Western:  -106.698837Eastern:  -106.698654
Geographic Region:
Description:White Sands crust sampling (549): Study 549 White Sands Missile Range crust samples: Gypsum soil, heavy lichen cover
Bounding Coordinates:
Northern:  32.729660Southern:  32.729660
Western:  -106.215882Eastern:  -106.215799
Geographic Region:
Description:Volcanic crust sampling (549): Study 549 Volcanic Site crust samples: On top of lava outcrop
Bounding Coordinates:
Northern:  32.105730Southern:  32.979502
Western:  -107.024705Eastern:  -107.024586

Project

Parent Project Information:

Title:Jornada Basin LTER
Personnel:
Individual:Dr. Niall Hanan
Address:
P.O. Box 30003, MSC 3JER,
New Mexico State University,
Las Cruces, NM 88003-8003 United States
Phone:
575-646-3335 (voice)
Email Address:
nhanan@nmsu.edu
Role:Principal Investigator
Abstract:

The Jornada Basin Long-Term Ecological Research (LTER) program is part of a national network of long-term ecological research sites funded by the US National Science Foundation (NSF). The Jornada LTER program has been continuously funded since 1982 to develop general principles governing changes between grassland and shrubland ecosystems based on long-term data collected in the Chihuahuan Desert. We translate our findings to dryland ecosystems around the world, and forecast the dynamics of future ecosystem states in response to changing climate and land use.

Funding:

JRN is funded by the National Science Foundation under award DEB 2025166.

Maintenance

Maintenance:
Description:completed
Frequency:asNeeded
Other Metadata

Additional Metadata

additionalMetadata
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        |___element 'metadata'
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        |     |___element 'unitList'
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        |     |     |     |___text '\n        '
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        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'abbreviation' = 'µmol/m²/s'
        |     |     |     |  \___attribute 'id' = 'micromolePerMeterSquaredPerSecond'
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        |     |     |     |  \___attribute 'abbreviation' = 'ml'
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        |     |     |     |     |___text '1/1000 of a liter'
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EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

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