Description
Please cite as: Naasko K.I., D.T. Naylor, E.B. Graham, S.P. Couvillion, R.E. Danczak, N. Tolic, and C.D. Nicora, et al. 2023. Influence of soil depth, moisture, and plants on multi-omic features and carbon chemistry in a calcareous soil: Summary Data. [Data Set] PNNL DataHub. https://doi.org/10.25584/PNNLDH/1985149
This file was created by Katherine Naasko (and edited by Bill Nelson)
GENERAL INFORMATION
1. Title of Dataset: Depth and moisture effects on soil chemistry and microbiome composition 2020 Naasko
2. Contributors:
Principal Investigator: Kirsten Hofmockel
Data contributor (creator, producer, etc): Katherine Naasko
3. Information about funding sources supporting the data: DOE BER GSP Soil Microbiome SFA, FWP
4. Geographic location of data collection: 46°15'04"N, 119°43'43"W, Prosser, WA, USA
5. Data History (single date, range, approximate date) <suggested format YYYY-MM-DD>:
A. Reporting Date:
B. Data activity type: Analyzing
D. Activity Reporter Contact Information (DataHub username, which is your Network ID)
E. Who is the data given to next (Contact Information (DataHub username, which is your Network ID)?:
DATA & FILE OVERVIEW
1. Data Activity Type Record:
A. File List:
1. metadata_Naasko.csv - soil sample environmental metadata_Naasko
2. lipids_Log2Norm_Naasko.csv - lipidomics results
3. metabolites_Log2Norm_Naasko.csv - metabolomics results
4. proteinAnn_Log2Norm_Naasko.csv - proteomics results with functional annotations
5. proteinKO_Log2Norm_Naasko.csv - proteomics results presented as summed counts for assigned KO families
6. 16S_CSSnorm_Naasko.csv - bacterial/archaeal amplicon analysis data
7. ITS_CSSnorm_Naasko.csv - fungal amplicon analysis data
B. Relationship between files, if important:
C. Additional related data collected that was not included in the current data package:
METHODOLOGICAL INFORMATION
1. Data Activity Type Record:
A. Description of methods used for collection/generation of data:
<Include links or references to publications or other documentation containing experimental design or protocols used in data collection>
These files contain multiomics, amplicon, and abiotic properties from 48 soil samples.
Samples were extracted from 4 treatments x 3 plots x (1 core/plot) from 0-1 meter
Cores were segmented into four depth increments 0-5 cm, 5-15 cm, 15-48 cm, 48-100 cm
B. Methods for processing the data:
<describe how the submitted data were generated from the raw or collected data>
Log2 transformation and central tendency (median) normalization performed on multi-omics
C. Instrument- or software-specific information needed to interpret the data:
<include full name and version of software, and any necessary packages or libraries needed to run scripts>
D. Standards and calibration information, if appropriate:
E. Environmental/experimental conditions:
WSU Irrigated Agriculture and Research Extension Center in Prosser, WA
July 20 and 21, 2020
F. Describe any quality-assurance procedures performed on the data:
DATA-SPECIFIC INFORMATION
1. metadata_Naasko2021.csv
A. Number of variables: 25
B. Number of cases/rows: 48
C. Variable List: <list variable name(s), description(s), unit(s)and value labels as appropriate for each>
SampleID Sample id
Plot Plot#
Treatment (Irr/NonIrr)(Alkar/Jose/Bare)
Irrigation Y (yes) or N (no)
Wheatgrass Y (yes) or N (no)
Variety Alkar or Jose Tall wheatgrass varieties
Landuse TWG (tall wheatgrass) or NP (not planted)
Depth_cm topdepth_bottomdepth in centimeters
MiD approximate mid-point depth of each horizon
TOC % Total organic carbon LECO TruSpec
TN % Total nitrogen LECO TruSpec
POXC % Permanganate oxidizable carbon Culman et al., 2012; microplate version
pH Soil pH 1:1 water:soil with calibrated electrode
SIC % Soil inorganic carbon LECO TruSpec on secondary acid pretreat samples
Moisture % Moisture Mass loss upon drying at 105C for 4 days
P ppm Olsen P Olsen phosphorus
SOM % Soil organic matter Walkley-black Method
K ppm Potassium NH4OAc (pH 8.5)
Ca ppm Calcium NH4OAc (pH 8.5)
Mg ppm Magnesium NH4OAc (pH 8.5)
Na ppm Sodium NH4OAc (pH 8.5)
S ppm Sulfur DTPA
Mn ppm Manganese DTPA
Zn ppm Zinc DTPA
Fe ppm Iron DTPA
D. Missing data codes: <list code/symbol and definition>n
E. Specialized formats or other abbreviations used:
2. lipids_Log2Norm_Naasko2021.csv
A. Number of variables: 48
B. Number of cases/rows: 649
C. Variable List:
Lipid Annotations include lipid class, number of carbons, and degrees of unsaturation per fatty acid
[one column for each sample] Pos & neg modes (LC/MS) were normalized individually then combined here.
D. Missing data codes: NA
E. Specialized formats or other abbreviations used:
3. metabolites_Log2Norm_Naasko2021.csv
A. Number of variables: 51
B. Number of cases/rows: 336
C. Variable List:
Metabolite Metabolite name assigned by MetaboAnalyst (polar metabolites detected by GC/MS)
KEGG KEGG compound ID
Class assigned by Naasko (Amino acid N-containing Nucleobase Ion Monosaccharide Polysaccharide Alcohol Organic acid Fatty acid Unknown CH(O) Unknown)
[one column per sample (48)]
D. Missing data codes: NA
E. Specialized formats or other abbreviations used:
4. proteinAnn_Log2Norm_Naasko2021.csv
A. Number of variables: 70
B. Number of cases/rows: 19164
C. Variable List:
FHT_Protein Protein ID linked to metagenome (WA2.5TmG)
FHT_Description Protein description generated in association with metagenome
[one column per sample (48)]
seed_ortholog id of closest sequence in SEED database
evalue evalue for similarity to SEED ortholog
score bit score for similarity to SEED ortholog
eggNOG_OGs eggNOG ortholog group
max_annot_lvl
COG_category COG functional category
Description eggNOG Description
Preferred_name gene symbol
GOs gene ontology terms
EC enzyme commission classification
KEGG_ko KEGG orthology group id
KEGG_Pathway KEGG pathway ids related to KO
KEGG_Module KEGG module ids related to KO
KEGG_Reaction KEGG reaction ids related to KO
KEGG_rclass KEGG reaction class ids related to KO
BRITE KEGG BRITE entry ids related to KO
KEGG_TC KEGG transporter classification
CAZy carbohydrate active enzyme classification
BiGG_Reaction BiGG reaction ids
PFAMs Pfam HMM classifications
D. Missing data codes: NA
E. Specialized formats or other abbreviations used:
5. proteinKO_Log2Norm_Naasko2021.csv
A. Number of variables: 49
B. Number of cases/rows: 1623
C. Variable List:
KO KEGG ortholog family id
[one column per sample (48)]
D. Missing data codes: NA
E. Specialized formats or other abbreviations used:
6. 16S_CSSnorm_Naasko.csv
A. Number of variables: 56
B. Number of cases/rows: 15829
C. Variable List:
[blank] arbitrary ASV id
[one column per sample (48)]
Domain taxonomic assignment levels by QIIME
Phylum
Class
Order
Family
Genus
Species
D. Missing data codes:
E. Specialized formats or other abbreviations used:
7. ITS_CSSnorm_Naasko.csv
A. Number of variables: 56
B. Number of cases/rows: 2556
C. Variable List:
[blank] arbitrary ASV id
[one column per sample (48)]
Domain taxonomic assignment levels by QIIME
Phylum
Class
Order
Family
Genus
Species
D. Missing data codes:
E. Specialized formats or other abbreviations used: