Data Package Metadata View Summary

Environmental context, microbial diversity, and microbial relative abundance data for biological soil crusts at four locations in the Chihuahuan desert near the Jornada Basin LTER site, 2020

General Information

Data Package:

Local Identifier:

knb-lter-jrn.210549001.5

Title:

Environmental context, microbial diversity, and microbial relative abundance data for biological soil crusts at four locations in the Chihuahuan desert near the Jornada Basin LTER site, 2020

Alternate Identifier:

DOI PLACE HOLDER

Abstract:

This dataset contains environmental and microbial diversity data relating to 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 ecology and microbial diversity of biocrust types at a range of Chihuahuan Desert sites, vegetation and soil data was collected along with soil crust samples at 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 type). After collection, crust samples were sequenced, targeting the 16S rRNA gene region for bacteria. This dataset includes the environmental context data, including vegetation cover (measured by the line-point intercept method) and soil chemistry data, as well as mean relative abundance for cyanobacterial species and phospholipid fatty acid analyses (PLFA) of crust samples for the purpose of comparing microbial biomass, biodiversity and functional type differences between different biocrust types at the four sites. Soil metagenomic data is hosted at the NCBI Sequence Read Archive, and links to those data are provided in an inventory file. This study is complete.

Short Name:

chihuahuan_crusts_env_microbialdiv

Publication Date:

2023-04-02

Language:

English

For more information:
Visit:	https://jrn.lternet.edu
Visit:	DOI PLACE HOLDER

Time Period

Begin:

2020-05-01

End:

2020-07-31

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

Data Entities
Data Table Name:	Data inventory table and NCBI links
Description:	Data inventory with links to NCBI accession numbers
Data Table Name:	LPI data
Description:	Line point intercept data from four Chihuahuan desert communities where biological soil crusts were collected for this study.
Data Table Name:	Soil chemistry data
Description:	Soil chemistry data sampled from 4 Chihuahan desert sites
Data Table Name:	Cyanobacterial abundance data
Description:	Cyanobacterial abundance data sampled from 4 Chihuahan desert sites
Data Table Name:	PLFA biomass data
Description:	Microbial biomass data derived from phospholipid fatty acid analysis at 4 Chihuahan desert sampling sites
Data Table Name:	Cover and species codes
Description:	Taxonomic codes for plants, soil crusts, and cover types used in the dataset, with links to USDA Plants codes when applicable

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549001/5/fcedc0c59920e750a6ced2bdb42e54a8
Name:	Data inventory table and NCBI links
Description:	Data inventory with links to NCBI accession numbers
Number of Records:	106
Number of Columns:	11

Table Structure

Object Name:

jrn549001_sample_and_ncbi_inventory.csv

Size:

16180 byte

Authentication:

53418405d2cee9ec77cc9f48c85ce00d Calculated By MD5

Text Format:

Number of Header Lines:

Number of Foot Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

BioProject ID

BioSample ID

BioSample link

SRA ID

SRA link

BioSample title

Local sample name

Sampling site

Biocrust type

Sample replicate

Collection date

Column Name:

bioproject_id

biosample_id

biosample_link

sra_id

sra_link

biosample_title

sample_name

Site

Type

SampleRep

collection_date

Definition:

NCBI BioProject database identifier

NCBI BioSample database identifier

URL for BioSample at NCBI

NCBI Sequence Read Archive identifier

URL for sequence data at NCBI

BioSample title

Sample name from BioSample metadata

Sampling site code

Crust type code

Sample replicate number

Date of sample collection

Storage Type:

string

integer

anyURI

integer

anyURI

string

integer

dateTime

Measurement Type:

nominal

ratio

nominal

ratio

nominal

ratio

dateTime

Measurement Values Domain:

Definition

any text

Unit	number
Type	integer

Definition

URL text

Unit	number
Type	integer

Definition

URL text

Definition

any text

Definition

any text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	JER
Definition	Jornada Experimental Range site (near T-WEST)
Source

Code Definition

Code	WHS
Definition	White Sands Missile Range site
Source

Code Definition

Code	VOL
Definition	Volcanic BLM site
Source

Code Definition

Code	AMT
Definition	A Mountain BLM site
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	DA
Definition	dark algal crust
Source

Code Definition

Code	PTL
Definition	Peltula lichen crust
Source

Code Definition

Code	MO
Definition	Moss crust
Source

Code Definition

Code	CVL
Definition	Clavascidium lichen crust
Source

Code Definition

Code	LA
Definition	light algal crust
Source

Unit	number
Type	integer

Format	YYYY-MM-DD
Precision	1

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549001/5/e057bbb3776f44c343ca6bc1dd2ce0e7
Name:	LPI data
Description:	Line point intercept data from four Chihuahuan desert communities where biological soil crusts were collected for this study.
Number of Records:	1200
Number of Columns:	7

Table Structure

Object Name:

jrn549001_LPI.csv

Size:

28247 byte

Authentication:

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Text Format:

Number of Header Lines:

Number of Foot Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Sampling site

Transect number

Line intercept point

Upper canopy code

Lower canopy code 1

Lower canopy code 2

Soil surface code

Column Name:

Site

Transect

Point

TopCanopy

Code1

Code2

SoilSurface

Definition:

Sampling site code

Transect number (1 or 2)

Point where observation was taken (every 0.2 m)

Plants in upper canopy

Plants in lower canopy

Soil surface cover

Storage Type:

string

integer

float

string

Measurement Type:

nominal

ratio

nominal

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	WHS
Definition	White Sands Missile Range site
Source

Code Definition

Code	VOL
Definition	Volcanic BLM site
Source

Code Definition

Code	JER
Definition	Jornada Experimental Range site (near T-WEST)
Source

Code Definition

Code	AMT
Definition	A Mountain BLM site
Source

Unit	number
Type	integer

Unit	meter
Type	real

Definition

any text

Definition

any text

Definition

any text

Definition

any text

Missing Value Code:

Code	NA
Expl	No vegetation

Code	NA
Expl	No vegetation

Code	NA
Expl	No vegetation

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549001/5/3b1c9404db9f2e889495d35ddc86df40
Name:	Soil chemistry data
Description:	Soil chemistry data sampled from 4 Chihuahan desert sites
Number of Records:	22
Number of Columns:	19

Table Structure

Object Name:

jrn549001_SoilChem.csv

Size:

1618 byte

Authentication:

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Text Format:

Number of Header Lines:

Number of Foot Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Sampling site

Biocrust type

Siol pH

Soluble salt

Excess lime

Organic matter loss

Nitrate N ppm

Phosphate P ppm

Potassium ppm

Sulfate S ppm

Calcium ppm

Magnesium ppm

Sodium ppm

Cation exchange capacity

%H Sat

%K Sat

%Ca Sat

%Mg Sat

%Na Sat

Column Name:

Site

Type

SSalt

Lime

OMLoss

NPPM

PPPM

KPPM

SPPM

CaPPM

MgPPM

NaPPM

CEC

HSat

KSat

CaSat

MgSat

NaSat

Definition:

Sampling site code

Crust type code

Soil pH value

Soluble salts 1:1

Excess Lime Rating, relative amount of soil effervescence

Organic Matter Loss on ignition

Nitrate N ppm N

Olsen P ppm P

Potassium ppm K

Sulfate-S ppm S

Calcium ppm Ca

Magnesium ppm Mg

Sodium ppm Na

Cation exchange capacity - Sum of Cations me/100g

%H Saturation

%K Saturation

%Ca Saturation

%Mg Saturation

%Na Saturation

Storage Type:

string

float

string

float

Measurement Type:

nominal

ratio

nominal

ratio

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	AMT
Definition	A Mountain BLM site
Source

Code Definition

Code	JER
Definition	Jornada Experimental Range site (near T-WEST)
Source

Code Definition

Code	VOL
Definition	Volcanic BLM site
Source

Code Definition

Code	WHS
Definition	White Sands Missile Range site
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	PTL
Definition	Peltula lichen crust
Source

Code Definition

Code	LA2
Definition	Light algal outlier collected under shrub (project 549)
Source

Code Definition

Code	PC
Definition	Physical crust (non-biological)
Source

Code Definition

Code	DA
Definition	dark algal crust
Source

Code Definition

Code	LA
Definition	light algal crust
Source

Code Definition

Code	CVL
Definition	Clavascidium lichen crust
Source

Code Definition

Code	MO
Definition	Moss crust
Source

Unit	pH
Type	real

Unit	millimhoPerCentimeter
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	HIGH
Definition	high soil lime content
Source

Code Definition

Code	LOW
Definition	low soil lime content
Source

Code Definition

Code	NONE
Definition	no soil lime detected
Source

Unit	percent
Type	real

Unit	partsPerMillion
Type	real

Unit	partsPerMillion
Type	real

Unit	partsPerMillion
Type	real

Unit	partsPerMillion
Type	real

Unit	partsPerMillion
Type	real

Unit	partsPerMillion
Type	real

Unit	partsPerMillion
Type	real

Unit	microequivalentsPer100g
Type	real

Unit	percent
Type	real

Unit	percent
Type	real

Unit	percent
Type	real

Unit	percent
Type	real

Unit	percent
Type	real

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549001/5/ed49c2a4d3221917d36e0ec15fd2d6bf
Name:	Cyanobacterial abundance data
Description:	Cyanobacterial abundance data sampled from 4 Chihuahan desert sites
Number of Records:	1800
Number of Columns:	11

Table Structure

Object Name:

jrn549001_CyanoAbundance.csv

Size:

249734 byte

Authentication:

bf415cb029c3bb218c207f6669f59cda Calculated By MD5

Text Format:

Number of Header Lines:

Number of Foot Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Amplicon sequence variant

Sampling site

Biocrust type

Relative abundance

Kingdom

Phylum

Class

Order

Family

Genus

Species

Column Name:

ASV

Site

Type

Abundance

Kingdom

Phylum

Class

Order

Family

Genus

Species

Definition:

Amplicon sequence variant

Sampling site code

Crust type code

Mean relative abundance of each species across 5 replicates

Taxonomic Kingdom name for ASV

Taxonomic Phylum name for ASV

Taxonomic Class name for ASV

Taxonomic Order name for ASV

Taxonomic Family name for ASV

Taxonomic genus name for ASV

Taxonomic species name for ASV. Taxonomic species name for ASV. Species relative abundance under 1% were renamed "<1% abund".

Storage Type:

string

float

string

Measurement Type:

nominal

ratio

nominal

Measurement Values Domain:

Definition

any text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	WHS
Definition	White Sands Missile Range site
Source

Code Definition

Code	VOL
Definition	Volcanic BLM site
Source

Code Definition

Code	JER
Definition	Jornada Experimental Range site (near T-WEST)
Source

Code Definition

Code	AMT
Definition	A Mountain BLM site
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	CVL
Definition	Clavascidium lichen crust
Source

Code Definition

Code	PTL
Definition	Peltula lichen crust
Source

Code Definition

Code	MO
Definition	Moss crust
Source

Code Definition

Code	LA
Definition	light algal crust
Source

Code Definition

Code	DA
Definition	dark algal crust
Source

Unit	fraction
Type	real

Definition

any text

Definition

any text

Definition

any text

Definition

any text

Definition

any text

Definition

any text

Definition

any text

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549001/5/4740bebc41a1ed7b4d377fa96fd2d709
Name:	PLFA biomass data
Description:	Microbial biomass data derived from phospholipid fatty acid analysis at 4 Chihuahan desert sampling sites
Number of Records:	20
Number of Columns:	31

Table Structure

Object Name:

jrn549001_PLFABiomass.csv

Size:

4344 byte

Authentication:

f3cf272a611907b4a990ab857c73d12f Calculated By MD5

Text Format:

Number of Header Lines:

Number of Foot Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Sampling site

Biocrust type

TotalBiomass

DiversityIndex

BacteriaPercent

BacteriaBiomass

ActinomycetesPercent

ActinomycetesBiomass

GramNegPercent

GramNegBiomass

RhizobiaPercent

RhizobiaBiomass

FungiPercent

FungiBiomass

ArbMycorrhizalPercent

ArbMycorrhizalBiomass

SaprophyticPercent

SaprophyticBiomass

ProtozoanPercent

ProtozoanBiomass

GramPosBiomass

GramPosPercent

UndifferentiatedPercent

UndifferentiatedBiomass

FungiToBacteria

PredatorToPrey

GramPosToGramNeg

SatToUnsat

MonoToPoly

Pre16ToCy17

Pre18ToCy19

Column Name:

Site

Type

TotalBiomass

DiversityIndex

BacteriaPercent

BacteriaBiomass

ActinomycetesPercent

ActinomycetesBiomass

GramNegPercent

GramNegBiomass

RhizobiaPercent

RhizobiaBiomass

FungiPercent

FungiBiomass

ArbMycorrhizalPercent

ArbMycorrhizalBiomass

SaprophyticPercent

SaprophyticBiomass

ProtozoanPercent

ProtozoanBiomass

GramPosBiomass

GramPosPercent

UndifferentiatedPercent

UndifferentiatedBiomass

FungiToBacteria

PredatorToPrey

GramPosToGramNeg

SatToUnsat

MonoToPoly

Pre16ToCy17

Pre18ToCy19

Definition:

Sampling site code

Crust type code

Total biomass

Simpson’s Diversity Index

Percent bacteria

Bacterial biomass

Percent Actinomyces

Actinomyces biomass

Gram Negative percent

Gram Negative biomass

Rhizobia percent

Rhizobia biomass

Percent fungi

Fungal biomass

Arbuscular mycorrhizal percent

Arbuscular mycorrhizal biomass

Saprophytic percent

Saprophytic biomass

Protozoan percent

Protozoa biomass

Gram positive biomass

Gram positive percent

Undifferentiated percent

Undifferentiated biomass

Fungi:Bacteria ratio

Predator:prey ratio

Gram positive:Gram negative ratio

Ratio of Saturated to Unsaturated fatty acids

Ratio of Mono to Polysaturated fatty acids

Pre 16:1w7c:cy17:0pre16 to cy17 fatty acids

Pre 18:1w7c:cy19:0pre18 to cy19 fatty acids

Storage Type:

string

float

string

float

string

Measurement Type:

nominal

ratio

nominal

ratio

nominal

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	JER
Definition	Jornada Experimental Range site (near T-WEST)
Source

Code Definition

Code	WHS
Definition	White Sands Missile Range site
Source

Code Definition

Code	VOL
Definition	Volcanic BLM site
Source

Code Definition

Code	AMT
Definition	A Mountain BLM site
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	DA
Definition	dark algal crust
Source

Code Definition

Code	LA
Definition	light algal crust
Source

Code Definition

Code	MO
Definition	Moss crust
Source

Code Definition

Code	PTL
Definition	Peltula lichen crust
Source

Code Definition

Code	CVL
Definition	Clavascidium lichen crust
Source

Unit	nanogramPerGram
Type	real

Unit	simpsonDivIndex
Type	real

Unit	percent
Type	real

Unit	nanogramPerGram
Type	real

Unit	percent
Type	real

Unit	nanogramPerGram
Type	real

Unit	percent
Type	real

Unit	nanogramPerGram
Type	real

Unit	percent
Type	real

Unit	nanogramPerGram
Type	real

Unit	percent
Type	real

Unit	nanogramPerGram
Type	real

Unit	percent
Type	real

Unit	nanogramPerGram
Type	real

Unit	percent
Type	real

Unit	nanogramPerGram
Type	real

Unit	percent
Type	real

Unit	nanogramPerGram
Type	real

Unit	nanogramPerGram
Type	real

Unit	percent
Type	real

Unit	percent
Type	real

Unit	nanogramPerGram
Type	real

Unit	dimensionless
Type	real

Definition

any text

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Definition

any text

Definition

any text

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/210549001/5/5a684a007adf2030c0c87a8ee2d94f88
Name:	Cover and species codes
Description:	Taxonomic codes for plants, soil crusts, and cover types used in the dataset, with links to USDA Plants codes when applicable
Number of Records:	46
Number of Columns:	3

Table Structure

Object Name:

jrn549001_LPI_codes.csv

Size:

1290 byte

Authentication:

de4e0db54f279e8b00d71555bb96bc05 Calculated By MD5

Text Format:

Number of Header Lines:

Number of Foot Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

LPI code

Code description

USDA Plants equivalent

Column Name:

LPI_code

description

USDA_plants_code

Definition:

Line point intercept code used in data files

Description of the species or cover indicated by the LPI code

Equivalent USDA Plants database code (if available)

Storage Type:

string

Measurement Type:

nominal

Measurement Values Domain:

Definition

any text

Definition

any text

Definition

any text

Missing Value Code:

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:
LTER Core Research Areas	populations
LTER Controlled Vocabulary v1	algae, bacterial abundance, community dynamics, deserts, genomics, grasses, microbial biomass, plant communities, shrubs, soil, soil chemistry, soil nutrients, soil organic matter, soil samples, species abundance, species diversity, transects
none	16S sequencing, biological, biotic crusts, cryptobiotic crusts, cyanobacteria, line-point intercept, lpi, relative abundance, soil crusts
Jornada Basin LTER dataset keywords	NCBI linked, non-core
Jornada Basin project names	study 549
Jornada Basin place names	T-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, replicate samples of 5 types of biological soil crusts were collected, along with representative soil samples and data on vegetation cover. Collections occurred between May and July of 2020 and samples were subsequently processed and analyzed using the following methods.

Preparation and metagenomic analysis (sequencing) of biological soil crust samples

At each of the four sites, five biocrust soil samples were collected for each of the five crust types (100 samples total). All soil crust samples were collected along the 2 intersecting 30 meter transects. Samples were stored in a -80C freezer until processing. Samples were homogenized by physically crushing the biocrust aggregate and shaking the collection bag until well mixed. A sample weight of ~0.25g biocrust soil was collected from each homogenized sample.Whole community genomic DNA was extracted from each crust type per site using DNeasy PowerLyzer Soil Kit by QIAGEN (Qiagen Laboratories, Carlsbad, CA, USA), with modification to the bead beating homogenizer step. Samples were subject to two 45sec interval and 5sec rest cycle in the Precellys 24 tissue homogenizer (Bertin Instruments, Paris, France) at 2500rpm. Some duplicate samples were added to the final well plate, for a total of 106 samples. Extracted DNA was sent to University of Minnesota Genomics Center for library preparation, amplification, and Illumina MiSeq. Illumina MiSeq sequencing occurred in 2x300 PE base format targeting 16S rRNA V4 gene region with the 515F and 806R primers following the protocol of the Earth Microbiome Project. Polymerase chain reaction (PCR) was performed with KAPA HiFidelity Hot Start Polymerase in a two step process. qPCR was carried out for quality checking with an initial denaturation 95ºC 5min, followed by 35 cycles of: denaturation 98ºC 20 sec, annealing 55ºC 15sec, and elongation 72ºC 1 min, followed by a final 70ºC 5min elongation and holding at 4ºC thereafter. Samples were then normalized to 167,000 molecules/ul. PCR1 was performed using the same steps as in qPCR but with 25 cycles. Samples were then diluted to 1:100 and 5ul were used in PCR2 where again the same steps were performed as in qPCR but using different forward and reverse indexing primer combinations and 10 cycles. Samples were pooled and denatured in 8 pM NaOH diluted in Illumina’s HT1 buffer, spiked with 15% PhiX. Heat denaturation was also carried out immediately before sample loading for 2min at 96ºC. Sequencing was performed using a MiSeq 600 cycle v3 kit. Post run trimming was carried out with Nextera adapter sequences. After demultiplexing, a total of 4,924,626 sequence reads were received in a range from 28-79381 per sample.

The raw sequence data can be found at the NCBI repository under BioProject #PRJNA748083, and metadata connecting NCBI sequence accessions to the sites and samples in this dataset can be found in the included data inventory table (JRN549001_sample_and_ncbi_inventory.csv).

Line Point Intercept data

Site characterization via line point intercept surveys (Herrick el al. 2016) was carried out along two transects at each of the 4 sites (May-July 2020). Surveys assessed plant and biocrust percent cover. Presence/absence of plant and/or biocrust type was recorded every 0.2m along 2 intersecting 30m transects (in X shape crossing at 15m). This information will be used to upscale carbon and nitrogen fixation rates to the landscape according to biocrust percent cover. Transects had a maximum of two codes between TopCanopy and SoilSurface, and cover codes used in the LPI data file are non-standard, so an explanatory table, with links to USDA Plants codes (https://plants.usda.gov) where applicable, are included in an attached file (JRN549001_LPI_codes.csv).

Soil chemistry data

To characterize soil chemical composition, composite soil samples (250g) were collected for each crust type at each site from 5 places along the 2 intersecting 30m transects. Samples were collected using sterile technique and stored at 4˚C until shipping to Ward Laboratories for analysis. Soil chemical analysis included CEC and Base Saturation (Haby et al. 1990 & Warncke et al. 1998), soil pH (Mc Lean 1982 & Watson & Brown 1998), soluble salt analysis (Rhoades 1982), loss on ignition (Combs & Nathan 1998), Mehlich 3 extract (Mehlich 1984 & Lachat instruments 2003, Rao & Sharma 1997), and H2O extract (Haney et al.1999, Haney et al. 2018).

Cyanobacterial abundance

Supercomputing was used to process sequencing data with standardized bioinformatics pipelines in Qiime2 (v2021.2) and AMPtk (v1.42). Briefly, the AMPtk program merged forward and reverse reads, binned samples according to barcode sequences, removed barcodes and primers, trimmed reads to 300 base pairs, clustered reads into ASVs with 97% similarity, and removed singleton ASVs.Bacterial taxonomy was assigned using Qiime2 pipeline and Silva (v138.1) (Bacteria and Archaea) database. Sequence data analyses were carried out in the R package phyloseq. Singletons and 9 samples with low read count were removed from the data set leaving a total of 4,922,472 sequences in a range of 10,753-79,381 sequences merged. ASVs were rarified to the minimum read count of 10,753. Chloroplast and mitochondrial data was removed and bacterial data was subsequently assessed for relative abundance of bacteria by Phylum. Cyanobacterial data was subset and manually reclassified using Cydrasil version 3.

PLFA Biomass

Broad taxonomic and functional group assignments of soil crust communities were made using phospholipid fatty acid (PLFA) analysis. Composite samples (250g) were collected for each crust type at each site from 5 places along the 2 intersecting 30m transects (in X shape crossing at 15m). Samples were collected using sterile technique and stored at 4˚C until shipping to Ward Laboratories for analysis. PLFA analysis was carried out using the procedure detailed in Stott (2019), based on the work of Buyer & Sasser (2012).

References

Buyer, J. S. & Sasser, M. (2012) High throughput phospholipid fatty acid analysis of soils. Applied Soil Ecology, 61, 127-130.

Combs, S. M. & Nathan, M. V. (1998) Soil Organic Matter. p. 53-58. J. R. Brown (ed.) Recommended Chemical Soil Test Procedures for the North Central Region. North Central Regional Publication No. 221 (revised). University of Missouri Ag. Exp. Station, Columbia, MO 65211.

Haby, V.A., Russelle, M.P. & Skoley, E.O. (1990) R. L. Westerman (ed.) Soil Testing and Plant Analysis (Third Edition), Testing Soils for Potassium, Calcium, and Magnesium. p. 181-227. Soil Sci. Soc. of Am., Madison, Wis.

Haney, R.L., Franzluebbers, A.J. Hons, F.M. & Zuberer, D.A. (1999) Soil C extracted with water or K2SO4: pH effect on determination of microbial biomass. Canadian Journal of Soil Science 79:529-533.

Haney, R.L., Haney, E.B., Smith, D.R., Harmel, R.D. & White, M.J. (2018) The soil health tool—Theory and initial broad-scale application, Applied Soil Ecology, Volume 125, Pages 162-168, ISSN 0929-1393, https://doi.org/10.1016/j.apsoil.2017.07.035.

Herrick, J. E., Van Zee, J. W., McCord, S. E., Courtright, E. M., Karl, J. W. & Burkett, L. M. (2016) Monitoring manual for grassland, shrubland, and savanna ecosystems. Volume I: Core Methods. USDA – ARS Jornada Experimental Range, Las Cruces, New Mexico.

Lachat Instruments (2003) QuickChem Automated Ion Analyzer Methods Manual. Determination of OrthoPhosphate in Bray or Mehlich Extracts of Soil by Flow Injection Analysis. QuickChem Method No. 12-115-01-1-A. Loveland, CO USA.

McLean, E.O. 1982. Soil pH and Lime Requirement. p. 199-223. In A. L. Page (ed.) Methods of Soil Analysis, Part 2.Chemical and Microbiological Properties-Agronomy Monograph no.9 (2nd edition). Soil Sci. Soc. of Am., Madison Wis.

Mehlich, A. (1984) Mehlich - 3 Soil Test Extractant: A Modification of Mehlich 2 Extractant. Commun. Soil Sci. Plant Anal., 15:1409-1416.

Rao, T. N. & Sharma, P. K. (1997) Evaluation of Mehlich III as an extractant for available soil sulfur, Communications in Soil Science and Plant Analysis, 28:13-14, 1033-1046, DOI: 10.1080/00103629709369853

Rhoades, J. D. (1982) A. L. Page (ed.) Methods of Soil Analysis, Part 2.Chemical and Microbiological Properties-Agronomy Monograph no.9 (2nd edition), Soluble Salts. p. 167-179. Soil Sci. Soc. of Am., Madison Wis.

Stott, D.E. 2019. Recommended Soil Health Indicators and Associated Laboratory Procedures. Soil Health Technical Note No. 450-03. U.S. Department of Agriculture, Natural Resources Conservation Service.

Warncke, D. & J. R. Brown J. R. (1998) J. R. Brown (ed.) Recommended Chemical Soil Test Procedures for the North Central Region. North Central Regional Publication No. 221 (revised), Potassium and Other Basic Cations p. 31-33. University of Missouri Ag. Exp. Station. Columbia, MO 65211

Watson, M. E. & J. R. Brown. (1998) J. R. Brown (ed.) Recommended Chemical Soil Test Procedures for the North Central Region. North Central Regional Publication No. 221 (revised), pH and Lime Requirement, p.13-16. University of Missouri Ag. Exp. Station. Columbia, MO 65211.

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:

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:

Information Manager

Phone:

575-322-2430

Email Address:

jornada.data@nmsu.edu

Web Address:

https://lter.jornada.nmsu.edu/information-management/

Associated Parties:

Individual:	Paul De Ley
Organization:	New Mexico State University
Role:	associate

Individual:	Andrew Dominguez
Organization:	New Mexico State University
Role:	associate

Metadata Providers:

Organization:

Jornada Basin LTER

Position:

Jornada Basin LTER program

Address:

P.O. Box 30003; MSC 3JER New Mexico State University,

Las Cruces, NM 88003-8003 USA

Email Address:

jornada.lter@nmsu.edu

Web Address:

https://lter.jornada.nmsu.edu

Id:

https://ror.org/05976ta47

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:	32.511184	Southern:	32.511065
Western:	-106.741358	Eastern:	-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:	32.300009	Southern:	32.300001
Western:	-106.698837	Eastern:	-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:	32.729705	Southern:	32.729715
Western:	106.215953	Eastern:	106.215950

Geographic Region:

Description:

Volcanic crust sampling (549): Study 549 Volcanic Site crust samples: On top of lava outcrop

Bounding Coordinates:

Northern:	32.105730	Southern:	32.979502
Western:	-107.024705	Eastern:	-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 (Current NSF award: DEB-2025166) 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.

Additional Award Information:

Funder:

National Science Foundation

Funder ID:

https://ror.org/05976ta47

Number:

2025166

Title:

LTER: Long –Term Research at the Jornada Basin (LTER VII)

URL:

https://www.nsf.gov/awardsearch/showAward?AWD_ID=2025166

Additional Award Information:

Funder:	National Science Foundation
Number:	DEB 1832194
Title:	Prior award: LTER: Long - Term Research at the Jornada Basin (LTER VII)

Additional Award Information:

Funder:	National Science Foundation
Number:	DEB 1235828
Title:	Prior award: LTER: Long-Term Research at the Jornada Basin (LTER-VI)

Additional Award Information:

Funder:	National Science Foundation
Number:	DEB 0618210
Title:	Prior award: Jornada Basin LTER V: Landscape Linkages in Arid and Semiarid Ecosystems

Additional Award Information:

Funder:	National Science Foundation
Number:	DEB 0080412
Title:	Prior award: LTER IV: Jornada Basin: Linkages in Semi-arid Landscapes

Additional Award Information:

Funder:	National Science Foundation
Number:	DEB 9411971
Title:	Prior award: LTER: The Chihuahuan Desert (The Jornada LTER III Consortium)

Additional Award Information:

Funder:	National Science Foundation
Number:	DEB 8811160, 9240261
Title:	Prior award: Interactions in Time and Space Variability in a Chihuahuan Desert Ecosystem: Jornada LTER (II)

Additional Award Information:

Funder:	National Science Foundation
Number:	DEB 8114466, 8612106
Title:	Prior award: Interactions of Time and Space Variability in a Chihuahuan Desert Ecosystem in New Mexico (Jornada LTER I)

Maintenance

Maintenance:

Description:	complete
Frequency:	asNeeded

Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'unitList'
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'dimensionless'
        |     |     |     |  \___attribute 'name' = 'dimensionless'
        |     |     |     |  \___attribute 'unitType' = 'dimensionless'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'a designation asserting the absence of an associated unit'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'abbreviation' = 'ng/g'
        |     |     |     |  \___attribute 'id' = 'nanogramPerGram'
        |     |     |     |  \___attribute 'multiplierToSI' = '0.000000001'
        |     |     |     |  \___attribute 'name' = 'nanogramPerGram'
        |     |     |     |  \___attribute 'parentSI' = 'gramPerGram'
        |     |     |     |  \___attribute 'unitType' = 'massPerMass'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'micrograms per gram'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'abbreviation' = 'µE/100g'
        |     |     |     |  \___attribute 'id' = 'microequivalentsPer100g'
        |     |     |     |  \___attribute 'name' = 'microequivalentsPer100g'
        |     |     |     |  \___attribute 'parentSI' = 'molePerMeterCubed'
        |     |     |     |  \___attribute 'unitType' = 'amountOfSubstanceConcentration'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'microequivalents per 100 g solution; concentration of charge (on dissolved ions). conversions must know the name of the ion; a single multiplier to SI is not possible'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'fraction'
        |     |     |     |  \___attribute 'multiplierToSI' = '1'
        |     |     |     |  \___attribute 'name' = 'fraction'
        |     |     |     |  \___attribute 'parentSI' = 'dimensionless'
        |     |     |     |  \___attribute 'unitType' = 'dimensionless'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'a decimal ratio of a part to a whole'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'number'
        |     |     |     |  \___attribute 'name' = 'number'
        |     |     |     |  \___attribute 'unitType' = 'dimensionless'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'a quantity or amount'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'abbreviation' = 'ppm'
        |     |     |     |  \___attribute 'id' = 'partsPerMillion'
        |     |     |     |  \___attribute 'multiplierToSI' = '1'
        |     |     |     |  \___attribute 'name' = 'partsPerMillion'
        |     |     |     |  \___attribute 'unitType' = 'dimensionless'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'ratio of two quantities as parts per million (1:1000000)'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'abbreviation' = '%'
        |     |     |     |  \___attribute 'id' = 'percent'
        |     |     |     |  \___attribute 'multiplierToSI' = '1'
        |     |     |     |  \___attribute 'name' = 'percent'
        |     |     |     |  \___attribute 'parentSI' = 'dimensionless'
        |     |     |     |  \___attribute 'unitType' = 'dimensionless'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'percent, one part per hundred parts. a decimal ratio multipled by 100'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'abbreviation' = 'm'
        |     |     |     |  \___attribute 'id' = 'meter'
        |     |     |     |  \___attribute 'multiplierToSI' = '1'
        |     |     |     |  \___attribute 'name' = 'meter'
        |     |     |     |  \___attribute 'unitType' = 'length'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'SI unit of length'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'abbreviation' = '-log([H+])'
        |     |     |     |  \___attribute 'id' = 'pH'
        |     |     |     |  \___attribute 'multiplierToSI' = '0'
        |     |     |     |  \___attribute 'name' = 'pH'
        |     |     |     |  \___attribute 'parentSI' = 'molesPerMole'
        |     |     |     |  \___attribute 'unitType' = 'dimensionless'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'Potential of Hydrogen (pH) measured as the negative logarithm of H+ concentration in solution'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'abbreviation' = 'mmhos/cm'
        |     |     |     |  \___attribute 'id' = 'millimhoPerCentimeter'
        |     |     |     |  \___attribute 'multiplierToSI' = '0.001'
        |     |     |     |  \___attribute 'name' = 'millimhoPerCentimeter'
        |     |     |     |  \___attribute 'parentSI' = 'siemens'
        |     |     |     |  \___attribute 'unitType' = 'conductance'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'electrical conductivity (usually in soil)'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'abbreviation' = 'SimpsonDiv'
        |     |     |     |  \___attribute 'id' = 'simpsonDivIndex'
        |     |     |     |  \___attribute 'multiplierToSI' = '1'
        |     |     |     |  \___attribute 'name' = 'simpsonDivIndex'
        |     |     |     |  \___attribute 'unitType' = 'dimensionless'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'Simpson\'s Diversity Index value'
        |     |     |     |___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

Environmental context, microbial diversity, and microbial relative abundance data for biological soil crusts at four locations in the Chihuahuan desert near the Jornada Basin LTER site, 2020

Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Package Usage Rights

Keywords

Methods and Protocols

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

Experimental and sampling design

Preparation and metagenomic analysis (sequencing) of biological soil crust samples

Line Point Intercept data

Soil chemistry data

Cyanobacterial abundance

PLFA Biomass

References

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Parent Project Information:

Maintenance

Additional Metadata

Recently Added

Recently Updated

Data Package Metadata View Summary

Environmental context, microbial diversity, and microbial relative abundance data for biological soil crusts at four locations in the Chihuahuan desert near the Jornada Basin LTER site, 2020

+/- Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

+/- Data Package Usage Rights

+/- Keywords

+/- Methods and Protocols

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

Experimental and sampling design

Preparation and metagenomic analysis (sequencing) of biological soil crust samples

Line Point Intercept data

Soil chemistry data

Cyanobacterial abundance

PLFA Biomass

References

+/- 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