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Title: From data to knowledge: The future of multi-omics data analysis for the rhizosphere

The rhizosphere is the interface between the root system of a plant and its surrounding soil. The microbiome of the rhizosphere, which is the totality of all microbes present there, represents a complex microbial ecosystem that nourishes the terrestrial biosphere. In order to untangle the complexity of the rhizosphere, and of the rhizospheric microbiome in particular, an integrated multi-omics approach can be applied to reveal the composition of the rhizospheric microbiome (through 16S ribosomal amplicons and metagenomics), the functional properties of the microbiome (through metatranscriptomics and metaproteomics), and the signaling network within the rhizosphere (through metametabolomics). The successful application of integrated multi-omics to rhizospheric science depends on the availability of rhizosphere-specific data and on the appropriate software used to analyze omics data from the rhizosphere. Here, we analyze the availability of software suites that are normally applied to surrogate disciplines (e.g., soil and plants) but which can be used for rhizospheric science. We also identify potential issues, challenges, and opportunities for rhizosphere science.
Authors:
 [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [2] ;  [1]
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Earth and Biological Sciences Directorate
  2. Graz Univ. of Technology (Austria). Inst. of Environmental Biotechnology
Publication Date:
Report Number(s):
PNNL-SA-125262
Journal ID: ISSN 2452-2198; PII: S2452219817300563
Grant/Contract Number:
AC05-76RL01830
Type:
Accepted Manuscript
Journal Name:
Rhizosphere
Additional Journal Information:
Journal Volume: 3; Journal Issue: 2; Journal ID: ISSN 2452-2198
Publisher:
Elsevier
Research Org:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; rhizosphere; multi-omics; metagenomics; metaproteomics; metabolomics
OSTI Identifier:
1355769

Allen White III, Richard, Borkum, Mark I., Rivas-Ubach, Albert, Bilbao, Aivett, Wendler, Jason P., Colby, Sean M., Köberl, Martina, and Jansson, Christer. From data to knowledge: The future of multi-omics data analysis for the rhizosphere. United States: N. p., Web. doi:10.1016/j.rhisph.2017.05.001.
Allen White III, Richard, Borkum, Mark I., Rivas-Ubach, Albert, Bilbao, Aivett, Wendler, Jason P., Colby, Sean M., Köberl, Martina, & Jansson, Christer. From data to knowledge: The future of multi-omics data analysis for the rhizosphere. United States. doi:10.1016/j.rhisph.2017.05.001.
Allen White III, Richard, Borkum, Mark I., Rivas-Ubach, Albert, Bilbao, Aivett, Wendler, Jason P., Colby, Sean M., Köberl, Martina, and Jansson, Christer. 2017. "From data to knowledge: The future of multi-omics data analysis for the rhizosphere". United States. doi:10.1016/j.rhisph.2017.05.001. https://www.osti.gov/servlets/purl/1355769.
@article{osti_1355769,
title = {From data to knowledge: The future of multi-omics data analysis for the rhizosphere},
author = {Allen White III, Richard and Borkum, Mark I. and Rivas-Ubach, Albert and Bilbao, Aivett and Wendler, Jason P. and Colby, Sean M. and Köberl, Martina and Jansson, Christer},
abstractNote = {The rhizosphere is the interface between the root system of a plant and its surrounding soil. The microbiome of the rhizosphere, which is the totality of all microbes present there, represents a complex microbial ecosystem that nourishes the terrestrial biosphere. In order to untangle the complexity of the rhizosphere, and of the rhizospheric microbiome in particular, an integrated multi-omics approach can be applied to reveal the composition of the rhizospheric microbiome (through 16S ribosomal amplicons and metagenomics), the functional properties of the microbiome (through metatranscriptomics and metaproteomics), and the signaling network within the rhizosphere (through metametabolomics). The successful application of integrated multi-omics to rhizospheric science depends on the availability of rhizosphere-specific data and on the appropriate software used to analyze omics data from the rhizosphere. Here, we analyze the availability of software suites that are normally applied to surrogate disciplines (e.g., soil and plants) but which can be used for rhizospheric science. We also identify potential issues, challenges, and opportunities for rhizosphere science.},
doi = {10.1016/j.rhisph.2017.05.001},
journal = {Rhizosphere},
number = 2,
volume = 3,
place = {United States},
year = {2017},
month = {5}
}