skip to main content


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.
ORCiD logo ; ; ORCiD logo ; ;
Publication Date:
Grant/Contract Number:
SC0012586; SC0012658; SC0018344; AC02-05CH11231; SC0014079; 1R01AI127850-01A1
Published Article
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 9; Journal Issue: 4; Related Information: CHORUS Timestamp: 2018-07-16 06:24:50; Journal ID: ISSN 2150-7511
American Society for Microbiology
Sponsoring Org:
Country of Publication:
United States
OSTI Identifier: