Data for Bandopadhyay et al., "Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces"
- Pacific Northwest National Laboratory (PNNL)
- Argonne National Laboratory
- University of Kentucky
- University of Toledo
These data are from Bandopadhyay et al., "Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces". This study aims to understand the soil microbial ecology along terrestrial-aquatic interfaces of a freshwater and estuarine region and how it relates to organic matter. We analyzed soil microbial (16S rRNA gene) and organic matter (Fourier-transform ion cyclotron resonance mass spectrometry, FTICR-MS) composition from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. This dataset includes 16S rRNA gene amplicon data (only processed file types included here) and organic matter composition from FTICR-MS data (raw and processed files included here) from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie and Chesapeake Bay regions. These sites are part of the COMPASS-FME project (https://compass.pnnl.gov/FME/COMPASSFME).File formats and software needed to access files: 16S rRNA gene amplicon data:These files follow the format reported here https://ess-dive.gitbook.io/amplicon-sequencing-reporting-format#updates-in-v1.0.1. As per this format, there are four file types reported:1. Taxon tables (also called sequence-by-sample or OTU (operational taxonomic unit)/ESV (exact sequence variant) tables) : available in a .txt file format and accessible using TextEdit or MS Excel.2. Representative sequences (also called consensus sequences) : available in a .fasta format and accessible using TextEdit.3. Sequencing metadata : available in a MS Excel workbook file format and CSV file format4. Bioinformatic metadata : available in a MS Excel workbook file format and CSV file formatFTICR-MS data:1. Raw data converted to a processed file with intensities of the peaks in the given samples : available in a MS Excel CSV file format2. Processed file used in analyses and visualizations (appended as icr_long_) : available in a MS Excel CSV file format3. Metadata file for ICR features (appended as icr_meta) : available in a MS Excel CSV file format
- Research Organization:
- COMPASS-FME
- Sponsoring Organization:
- U.S. DOE > Office of Science > Biological and Environmental Research (BER)
- DOE Contract Number:
- AC02-05CH11231
- OSTI ID:
- 2589181
- Country of Publication:
- United States
- Language:
- English
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16S rRNA Amplicon sequence data and community assembly process file
Related Subjects
EARTH SCIENCE > BIOSPHERE > ECOLOGICAL DYNAMICS
EARTH SCIENCE > LAND SURFACE > SOILS
EARTH SCIENCE > LAND SURFACE > SOILS > MICROFAUNA
EARTH SCIENCE > OCEANS > COASTAL PROCESSES
ESS-DIVE Amplicon Sequencing Reporting Format
ESS-DIVE CSV File Formatting Guidelines Reporting Format
ESS-DIVE File Level Metadata Reporting Format