Dataset - Metabolomics, Amplicon (16S, ITS), Computed Analysis RhizoGrid Indexed Sorghum Rhizosphere Multi-Omics

RhizoGrid Indexed Sorghum Rhizosphere Multi-Omics

pending public release

Identification of spatially resolved biomarkers of drought in Sorghum bicolor rhizosphere molecular-microbe interactions using a novel root cartography "RhizoGrid" system for sampling plants under drought and control conditions across 10 equally sized root zone environments (4 quadrants each). Each quadrant was sampled and processed for 16S amplicon, metabolomics, and X-ray computed tomography (XCT). 

Accessible Digital Data Downloads

RhizoGrid Multi-Omics Data Files

1. Liquid chromatography mass spectrometry (LC-MS) metabolomics analysis of microbial community root exudates
2. Next-generation sequencing (NGS) 16S rRNA sequence analysis of microbial community assembly
3. X-ray computed tomography (XCT) spatial gradient analysis of microbial community composition (raw files, 3D spatial images and videos, root measurement data, and model input data)

The source code notebook used for evaluation of microbial community key taxa and spatially resolved root exudate data can be found at 10.5281/zenodo.17634932, supporting data processing transparency.
 

Linked Primary Data Accessions

Mass Spectrometry

• MassIVE: MSV000100162

Sequencing

• BioProject: PRJNA1378811
• SRA: SRP654059

Funding Acknowledgments

This research was supported in part by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research (BER), as part of the Genomic Science Program Secure Biosystems Design Science Focus Area Project: Persistence Control of Engineered Functions in Complex Soil Microbiomes (PerCon SFA) as a contribution of Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated by Battelle for the DOE under Contract No. DE-AC05-76RL01830. A portion of this research was supported under the EMSL user project award 10.46936/cpcy.proj.2022.60649/60008751, in leveraging instrument capabilities operating at the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility, sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830.

Citation Policy

In efforts to enable discovery and reproducibility of PerCon SFA project-funded digital data assets listed at the PNNL DataHub institutional repository, we kindly ask any reuse of project data download materials acknowledge all primary and secondary dataset citations and corresponding journal articles where applicable in accordance with community best practices (e.g., FORCE11 Data Citation Principles). Reference citations, should provide the necessary metadata information required to support, corroborate, verify, and otherwise determine the legitimacy of the research findings provided (data and code) from scholarly publications and corresponding project data releases.

Data Licensing

Creative Commons Attribution 4.0 International (CC BY 4.0)