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

Allen White III, Richard; Borkum, Mark I.; Rivas-Ubach, Albert; Bilbao, Aivett; Wendler, Jason P.; Colby, Sean M.; Köberl, Martina; Jansson, Christer

doi:10.1016/j.rhisph.2017.05.001

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

Journal Article · Thu May 04 00:00:00 EDT 2017 · Rhizosphere

DOI:https://doi.org/10.1016/j.rhisph.2017.05.001· OSTI ID:1355769

Allen White III, Richard ^[1]; Borkum, Mark I. ^[1]; Rivas-Ubach, Albert ^[1]; Bilbao, Aivett ^[1]; Wendler, Jason P. ^[1]; Colby, Sean M. ^[1]; Köberl, Martina ^[2]; Jansson, Christer ^[1]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Earth and Biological Sciences Directorate
Graz Univ. of Technology (Austria). Inst. of Environmental Biotechnology

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.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1355769

Alternate ID(s):: OSTI ID: 1496480

Report Number(s):: PNNL-SA-125262; PII: S2452219817300563

Journal Information:: Rhizosphere, Vol. 3, Issue 2; ISSN 2452-2198

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 13 works

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