Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry
Abstract
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.
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Johns Hopkins Univ., Baltimore, MD (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); 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. https://doi.org/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. https://doi.org/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 = {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.},
doi = {10.1128/mBio.01175-18},
journal = {mBio (Online)},
number = 4,
volume = 9,
place = {United States},
year = {Tue Jul 17 00:00:00 EDT 2018},
month = {Tue Jul 17 00:00:00 EDT 2018}
}
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https://doi.org/10.1128/mBio.01175-18
https://doi.org/10.1128/mBio.01175-18
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Cited by: 29 works
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Figures / Tables:
Figure 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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