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Title: The soil microbiome — from metagenomics to metaphenomics

Abstract

Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiome and available resources. Here in this paper we describe examples of opportunities towards gaining understanding of the soil metaphenome.

Authors:
;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1437832
Alternate Identifier(s):
OSTI ID: 1422511
Report Number(s):
PNNL-SA-132057
Journal ID: ISSN 1369-5274; S1369527417302205; PII: S1369527417302205
Grant/Contract Number:  
AC05-76RLO1830; AC05-76RL01830
Resource Type:
Published Article
Journal Name:
Current Opinion in Microbiology
Additional Journal Information:
Journal Name: Current Opinion in Microbiology Journal Volume: 43 Journal Issue: C; Journal ID: ISSN 1369-5274
Publisher:
Elsevier
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Jansson, Janet K., and Hofmockel, Kirsten S. The soil microbiome — from metagenomics to metaphenomics. United Kingdom: N. p., 2018. Web. doi:10.1016/j.mib.2018.01.013.
Jansson, Janet K., & Hofmockel, Kirsten S. The soil microbiome — from metagenomics to metaphenomics. United Kingdom. doi:10.1016/j.mib.2018.01.013.
Jansson, Janet K., and Hofmockel, Kirsten S. Fri . "The soil microbiome — from metagenomics to metaphenomics". United Kingdom. doi:10.1016/j.mib.2018.01.013.
@article{osti_1437832,
title = {The soil microbiome — from metagenomics to metaphenomics},
author = {Jansson, Janet K. and Hofmockel, Kirsten S.},
abstractNote = {Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiome and available resources. Here in this paper we describe examples of opportunities towards gaining understanding of the soil metaphenome.},
doi = {10.1016/j.mib.2018.01.013},
journal = {Current Opinion in Microbiology},
number = C,
volume = 43,
place = {United Kingdom},
year = {2018},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1016/j.mib.2018.01.013

Citation Metrics:
Cited by: 15 works
Citation information provided by
Web of Science

Figures / Tables:

Figure 1 Figure 1: Illustrative overview of biotic and environmental factors contributing to the soil metaphenome. A cross section of a field is shown with different soil moisture levels. On the right side, plant growth is constrained due to low soil moisture levels. An example of a measurable phenotype is shown (CO2,more » corresponding to soil respiration), which is the result of combined metabolic interactions between soil microbes and plants. Call out circles correspond to a microscale view of soil consortia residing in spatially discrete soil aggregates. Connectivity between consortia is determined by the extent of the pore volume that is water filled and available for diffusion of chemical signals and metabolites. Bacterial (purple symbols) interactions within consortia are designated with white arrows. Fungal hyphae (green filaments) may bridge spatially discrete consortia. Soil viruses (orange symbols) also play a yet undefined role in regulating the soil metaphenome. Lower panel illustrates different types of models applicable to defining the soil metaphenome; from left to right: biochemical reaction networks squares correspond to bacterial (purple) or fungal (green) metabolites, interspecies interaction networks, and interkingdom interactions« less

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Works referencing / citing this record:

The Serendipitous Value of Soil Fauna in Ecosystem Functioning: The Unexplained Explained
journal, December 2018


Climate change microbiology — problems and perspectives
journal, May 2019

  • Hutchins, David A.; Jansson, Janet K.; Remais, Justin V.
  • Nature Reviews Microbiology, Vol. 17, Issue 6
  • DOI: 10.1038/s41579-019-0178-5

Climate change microbiology — problems and perspectives
journal, May 2019

  • Hutchins, David A.; Jansson, Janet K.; Remais, Justin V.
  • Nature Reviews Microbiology, Vol. 17, Issue 6
  • DOI: 10.1038/s41579-019-0178-5

The Serendipitous Value of Soil Fauna in Ecosystem Functioning: The Unexplained Explained
journal, December 2018


    Figures / Tables found in this record:

      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.