Dataset - Omics, Metabolomics, Lipidomics, Amplicon (16S, ITS) WA-Omics_LA.1.0 (Metabolomics, Lipidomics, & Amplicon 16S/ITS, WA)

Multi-Omics Extended Data Package DOI

Rapid Remodeling of the Soil Lipidome in Response to a Drying-Rewetting Event

This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. Drought induced nutrient limitation was reflected in the lipidome and polar metabalome, both of which rapidly shifted  (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long chain polyunsaturated fatty acids, in dry soil suggests that lipids play an important role in fungal drought tolerance. Increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions.

Data package contents reported here are the first version and contain pre- and post-processed data acquisition and subsequent downstream analysis files using various data source instrument method techniques and Mass Spectroscopy (MS) EMSL capabilities. This publication data package DOI is a comprehensive high-throughput multi-omics data lifecycle collection containing processed data method metadata. Support files include additional data download “Read Me” file containing data descriptor information and data source application ontologies (see data dictionary). Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, GC-MS/LC-MS mass spectrometry datasets (Thermo .raw) were deposited at the MassIVE database repository under the related data accession MSV000086931 and can be accessed by using the API. Statistical data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location. 

Content Contributors

• LN Anderson (0000-0002-8741-7823) - Content Author, Curator
• M Pleake (0000-0002-7807-8364) - IT Engineering, RDM Support

STANDARD SUPPORT FILES

• "Read Me" data package content files (doc, txt)
• Standard structured metadata files (xls, json, xml)
• SwissLipids species ontology identifiers (csv)
• Processed data analysis R markdown (html, Rmd)

LINKED DATABASE IDENTIFIERS

• Mass Spectrometry Accession: MSV000086931 | ftp://massive.ucsd.edu/MSV000086931 (18.73 GB) (same as 10.25345/C5K50H)
• Amplicon Sequencing Accession: Sequence Read Archive (accession pending)

DATA TYPES AVAILABLE AT DOWNLOAD

Total Download Size: > 21 GB for > 340 items (210 raw instrument data files total)

KEY: Data Acquisition Method | ID | Format (raw instrument data file count)

1. Amplicon Sequencing (16S/ITS) | EFO:0005087 | fastq (120 raw read datasets)
2. Liquid Chromatography Mass Spectrometry (LC-ESI-MS/MS) | MS:1000856 | raw/mzML (60 polar lipid datasets)
3. Gas Chromatography Mass Spectrometry (GC-MS) | MS:1002802 | raw/cdf (30 polar metabolite datasets)

DOWNLOADABLE FILE FORMATS

• Raw data files (cdf, mzML, fastq)
• Processed data files (Rmd, biom, fasta, txt, csv, xlsx, mzXML)
• Image object files (pdf)
• Metadata collection files (html, xlsx, csv)
• Technical parameters/specification files (csv, xml)
• Molecular Network (cys, html)

RELATED SOFTWARE METHODS

• LIQUID LC-MS Analysis Software | 10.5281/zenodo.6459462
• Lipid Mini-On Software Tools (Lipid Mining and Ontology) | 10.5281/zenodo.1492803
• GNPS
• MZmine 2
• Cytoscape
• pmartR Omics Statistical Software | 10.5281/zenodo.6108667
• QIIME2 (v2021.4)
• SILVA Database (v138)
• UNITE Database (v8-10.05.2021)

ACKNOWLEDGEMENTS

This research was supported by the U.S. Department of Energy (DOE) under the Biological and Environmental Research (BER) and Genomic Science Program (GSP), and is a contribution of the Pacific Northwest National Laboratory (PNNL) Scientific Focus Area: "Phenotypic response of the soil microbiome to environmental perturbations" project. A portion of this project research was performed on a project award (10.46936/cpcy.proj.2021.60161/60000437) from the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830.