KS4A-Omics1.0_FspDS682 (Fungal Monoisolate Multi-Omics Proteome, KS)

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KS4A-Omics1.0_FspDS68 Fungal Monoisolate Multi-Omics Data Package DOI

"Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization" 

Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils, because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hotspots. However, the molecular mechanisms underlying fungal mineral weathering and transport through soil remains poorly understood. Here, we addressed this knowledge gap by directly visualizing nutrient acquisition and transport through fungal hyphae in a mineral doped soil micromodel using a multimodal imaging approach. Here, we observed how a representative of common saprotrophic soil fungi, Fusarium sp. DS 682, exhibited a mechanosensory response (thigmotropism) around obstacles and through pore spaces (~12 μm) in the presence of minerals.This study establishes the significance of fungal biology and nutrient translocation mechanisms in maintaining fungal growth under water and nutrient limitations in a soil-like microenvironment, using a high-throughput multi-omic analysis approach.

 

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 for Mass Spectroscopy, Mass Spectrometry, Microscopy, and Optimal Imaging EMSL capabilities. This data package DOI is a comprehensive collection of high-throughput multi-omics data and process method metadata. Support files include additional data download “Read Me”  file inclusive of dataset descriptor information and source method application ontologies (see data dictionary). Reported data download contents are structured for compliance with reported guidelines provided by community standard initiatives and publisher stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, novel fungal isolate Fusarium sp. DS 682 mass spectrometry datasets (Thermo .raw ) have been deposited at the MassIVE database repository under the related data accession MSV000087221 and can be accessed by API from the Datahub data download button. Statistical software data processing workflow and resulting interactive trelliscope plots can be found at the GitHub repository Fusarium sp. DS682 Proteogenomics.

 

DATA PACKAGE SUPPORT FILES

  • Data package contents and dataset key "Read Me" file (.doc)
  • Data Dictionary for Controlled Vocabularies & Ontologies (.obo)
  • Standard Metadata Reporting Guidelines (MIGS + MIAPE) (.json, .xml)
  • Fusarium sp. DS 682 Protein Sequence Annotations (Updated GenBank Locus Tag IDs) (.fasta)
  • Comprehensive Proteogenomic Annotations & KEGG Mapping (.png)
  • Statistical Proteomics Analysis & Interactive Trelliscope Plots (GitHub Page) (.Rproj/.Rmd)

 

DATA TYPES AVAILABLE AT DOWNLOAD

Size: 16.62 GB for 156 items (Acquisition Method | Ontology ID | Data File Format)

  1. Time-of-Flight Secondary Ion Mass Spectroscopy (ToF-SIMS) | CHMO:0000565 | ita, itm, jpg
  2. Liquid Chromatography Mass Spectrometry (LC-MS) | MS:1002634 | raw, mzML
  3. X-Ray Diffraction (XRD) | CHMO:0001138 | asc, xrdml
  4. X-Ray Photoelectron Spectroscopy (XPS) | CHMO:0000404 | csv, docx
  5. X-Ray Absorption Near Edge Structure Spectroscopy (XANES) | CHMO:0000305 | dat, nor/avg.nor, xlsx
  6. Micro-X-Ray Fluorescence Microscopy (XRF) | CHMO:0002311 | hdf5
  7. Scanning Electron Microscopy (SEM) | CHMO:0000073 | tiff, pdf
  8. Optical Microscopy (OM) | CHMO:0000102 | tiff, jpg

DOWNLOADABLE FILE FORMATS

  • Raw data files (raw, itm)
  • Processed data files (mzML, dat, txt, csv)
  • Depth profile data files (ita)
  • Image files (jpg, tiff, dat, hdf5)
  • Information files (docx, pdf, xlsx)
  • Parameter files (json, xml)
  • Sequence record annotation files (fasta)

 

LINKED DATA/DATABASES

 

RELATED SOFTWARE METHODS

 

ACKNOWLEDGEMENTS

This research was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research (BER) and is a contribution of the Scientific Focus Area "Phenotypic response of the soil microbiome to environmental perturbations." Pacific Northwest National Laboratory (PNNL) is operated for the DOE by Battelle Memorial Institute under Contract DE-AC05-76RLO1830. A portion of the research was performed using the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by the BER and located at PNNL.

Use of the Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, is supported by the DOE, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE-BER, and by the National Institutes of Health (NIH), National Institute of General Medical Sciences (NIGMS, P30GM133894). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH.

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Lindsey Anderson’s research has been dedicated to the identification and characterization of novel, targeted and non-targeted, functional metabolic interactions using a high-throughput systems biology and computational biology approach. Her expertise in functional metabolism and multidisciplinary...

Materials Scientist and Bioengineer with extensive experience in Microfabrication, Biofilm engineering, Microfluidics and Microbiology assay development. Primary areas of interest include photolithography, microfluidics, Biological imaging and Biomaterials.

Chris received his Bachelor of Science degree in chemistry at the University of Colorado at Colorado Springs in 2005. He attained his PhD in chemistry at the University of Illinois at Urbana–Champaign in 2011, under Mary L. Kraft, where his graduate work focused on using secondary ion mass...

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