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Title: Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry

Abstract

The chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities because genome annotations and functions are derived from the minority of microbes that have been propagated in the laboratory. Yet the diversity, complexity, inaccessibility, and irreproducibility of native microbial consortia limit our ability to interpret chemical signaling and map metabolic networks. In this perspective, we contend that standardized laboratory ecosystems are needed to dissect the chemistry of soil microbiomes. We argue that dissemination and application of standardized laboratory ecosystems will be transformative for the field, much like how model organisms have played critical roles in advancing biochemistry and molecular and cellular biology. Community consensus on fabricated ecosystems (“EcoFABs”) along with protocols and data standards will integrate efforts and enable rapid improvements in our understanding of the biochemical ecology of microbial communities.

Authors:
ORCiD logo; ; ORCiD logo; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Johns Hopkins Univ., Baltimore, MD (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); USDOE Office of Energy Efficiency and Renewable Energy (EERE)
OSTI Identifier:
1460472
Alternate Identifier(s):
OSTI ID: 1478345; OSTI ID: 1485593
Grant/Contract Number:  
SC0012586; SC0012658; SC0018344; AC02-05CH11231; SC0014079
Resource Type:
Published Article
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online) Journal Volume: 9 Journal Issue: 4; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; chemistry of soil microbiomes; exometabolomics; laboratory ecosystems; metabolic networks; synthetic communities

Citation Formats

Zhalnina, Kateryna, Zengler, Karsten, Newman, Dianne, Northen, Trent R., and Davies, ed., Julian E. Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry. United States: N. p., 2018. Web. doi:10.1128/mBio.01175-18.
Zhalnina, Kateryna, Zengler, Karsten, Newman, Dianne, Northen, Trent R., & Davies, ed., Julian E. Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry. United States. doi:10.1128/mBio.01175-18.
Zhalnina, Kateryna, Zengler, Karsten, Newman, Dianne, Northen, Trent R., and Davies, ed., Julian E. Tue . "Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry". United States. doi:10.1128/mBio.01175-18.
@article{osti_1460472,
title = {Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry},
author = {Zhalnina, Kateryna and Zengler, Karsten and Newman, Dianne and Northen, Trent R. and Davies, ed., Julian E.},
abstractNote = {The chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities because genome annotations and functions are derived from the minority of microbes that have been propagated in the laboratory. Yet the diversity, complexity, inaccessibility, and irreproducibility of native microbial consortia limit our ability to interpret chemical signaling and map metabolic networks. In this perspective, we contend that standardized laboratory ecosystems are needed to dissect the chemistry of soil microbiomes. We argue that dissemination and application of standardized laboratory ecosystems will be transformative for the field, much like how model organisms have played critical roles in advancing biochemistry and molecular and cellular biology. Community consensus on fabricated ecosystems (“EcoFABs”) along with protocols and data standards will integrate efforts and enable rapid improvements in our understanding of the biochemical ecology of microbial communities.},
doi = {10.1128/mBio.01175-18},
journal = {mBio (Online)},
number = 4,
volume = 9,
place = {United States},
year = {2018},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1128/mBio.01175-18

Citation Metrics:
Cited by: 7 works
Citation information provided by
Web of Science

Figures / Tables:

FIG 1 FIG 1: (A) Metabolites are the currency and communication for microbial communities. (B) Model laboratory ecosystems for discovering causal mechanisms of connections between genes and metabolites governing plant-microbe interactions.

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    Works referencing / citing this record:

    Modelling approaches for studying the microbiome
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      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.