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

Zhalnina, Kateryna; Zengler, Karsten; Newman, Dianne; Northen, Trent R.

doi:10.1128/mBio.01175-18

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

Journal Article · 17 July 2018 · mBio (Online)

DOI: https://doi.org/10.1128/mBio.01175-18 · OSTI ID:1460472

^[1]; Zengler, Karsten ^[2];

^[3]; Northen, Trent R. ^[1]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of California, San Diego, CA (United States). Center for Microbiome Innovation
California Inst. of Technology (CalTech), Pasadena, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Johns Hopkins Univ., Baltimore, MD (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE; USDOE Office of Energy Efficiency and Renewable Energy (EERE)

Grant/Contract Number:: AC02-05CH11231; SC0014079; SC0012586; SC0012658; SC0018344

OSTI ID:: 1460472

Alternate ID(s):: OSTI ID: 1478345; OSTI ID: 1485593

Journal Information:: mBio (Online), Vol. 9, Issue 4; ISSN 2150-7511

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 29 works

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Related Subjects

54 ENVIRONMENTAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
chemistry of soil microbiomes
exometabolomics
laboratory ecosystems
metabolic networks
synthetic communities