Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

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 Office of Science (SC), Biological and Environmental Research (BER)
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:  
AC05-76RL01830
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.
Copy to clipboard
Jansson, Janet K., & Hofmockel, Kirsten S. The soil microbiome — from metagenomics to metaphenomics. United Kingdom. https://doi.org/10.1016/j.mib.2018.01.013
Copy to clipboard
Jansson, Janet K., and Hofmockel, Kirsten S. Fri . "The soil microbiome — from metagenomics to metaphenomics". United Kingdom. https://doi.org/10.1016/j.mib.2018.01.013.
Copy to clipboard
@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}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.mib.2018.01.013
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 192 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
All figures and tables (2 total)
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

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

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
journal, October 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

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
journal, October 2018

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

Microbiome and imputed metagenome study of crude and refined petroleum-oil-contaminated soils: Potential for hydrocarbon degradation and plant-growth promotion
journal, September 2019

  • Auti, Asim M.; Narwade, Nitin P.; Deshpande, Neelima M.
  • Journal of Biosciences, Vol. 44, Issue 5
  • DOI: 10.1007/s12038-019-9936-9

Common principles and best practices for engineering microbiomes
journal, September 2019

  • Lawson, Christopher E.; Harcombe, William R.; Hatzenpichler, Roland
  • Nature Reviews Microbiology, Vol. 17, Issue 12
  • DOI: 10.1038/s41579-019-0255-9

Soil microbiomes and climate change
journal, October 2019

Cell-to-cell bacterial interactions promoted by drier conditions on soil surfaces
journal, September 2018

  • Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 39
  • DOI: 10.1073/pnas.1808274115

Effect of Capsicum annuum cultivated in sub-alkaline soil on bacterial community and activities of cultivable plant growth promoting bacteria under field conditions
journal, January 2019

  • Khenaka, Karima; Canfora, Loredana; Benedetti, Anna
  • Archives of Agronomy and Soil Science, Vol. 65, Issue 10
  • DOI: 10.1080/03650340.2019.1566711

Organic Soils Control Beetle Survival While Competitors Limit Aphid Population Growth
journal, September 2019

  • Krey, Karol L.; Blubaugh, Carmen K.; Van Leuven, James T.
  • Environmental Entomology, Vol. 48, Issue 6
  • DOI: 10.1093/ee/nvz100

Zones of influence for soil organic matter dynamics: A conceptual framework for data and models
journal, August 2019

  • Cagnarini, Claudia; Blyth, Eleanor; Emmett, Bridget A.
  • Global Change Biology, Vol. 25, Issue 12
  • DOI: 10.1111/gcb.14787

Systematic analysis of the Myxococcus xanthus developmental gene regulatory network supports posttranslational regulation of FruA by C‐signaling
journal, April 2019

  • Saha, Shreya; Patra, Pintu; Igoshin, Oleg
  • Molecular Microbiology, Vol. 111, Issue 6
  • DOI: 10.1111/mmi.14249

Soil physiology discriminates between no‐till agricultural soils with different crop systems on winter season
journal, January 2020

  • Frene, Juan P.; Gabbarini, Luciano A.; Wall, Luis G.
  • Soil Use and Management, Vol. 36, Issue 4
  • DOI: 10.1111/sum.12568

MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms
journal, January 2018

Challenges and Approaches in Microbiome Research: From Fundamental to Applied
journal, August 2018

Differences in Bacterial Diversity, Composition and Function due to Long-Term Agriculture in Soils in the Eastern Free State of South Africa
journal, April 2019

  • Dube, Joel P.; Valverde, Angel; Steyn, Joachim M.
  • Diversity, Vol. 11, Issue 4
  • DOI: 10.3390/d11040061

Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era
journal, August 2019

Fertigation: Nutrition, Stimulation and Bioprotection of the Root in High Performance
journal, October 2018

  • García-Gaytán, Víctor; Hernández-Mendoza, Fanny; Coria-Téllez, Ana
  • Plants, Vol. 7, Issue 4
  • DOI: 10.3390/plants7040088

Analysis of Soil Properties, Bacterial Community Composition, and Metabolic Diversity in Fluvisols of a Floodplain Area
journal, July 2019

  • Furtak, Karolina; Grządziel, Jarosław; Gałązka, Anna
  • Sustainability, Vol. 11, Issue 14
  • DOI: 10.3390/su11143929

Identification of new microbial functional standards for soil quality assessment
journal, January 2020

  • Thiele-Bruhn, Sören; Schloter, Michael; Wilke, Berndt-Michael
  • SOIL, Vol. 6, Issue 1
  • DOI: 10.5194/soil-6-17-2020
    Sort by:
    [ × clear filter / sort ]

    Figures / Tables found in this record:

    Figure 1 (p. 3)figure
    Figure 2 (p. 4)figure
      [ × clear filter / sort ]
      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.

      Similar Records in DOE PAGES and OSTI.GOV collections: