A Caltech Library Service

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

Zhalnina, Kateryna and Zengler, Karsten and Newman, Dianne and Northen, Trent R. (2018) Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry. mBio, 9 (4). Art. No. e01175-18. ISSN 2150-7511. PMCID PMC6050955.

[img] PDF - Published Version
Creative Commons Attribution.


Use this Persistent URL to link to this item:


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.

Item Type:Article
Related URLs:
URLURL TypeDescription CentralArticle
Newman, Dianne0000-0003-1647-1918
Additional Information:Copyright © 2018 Zhalnina et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Received 1 June 2018 Accepted 8 June 2018 Published 17 July 2018. T. Northen and K. Zhalnina gratefully acknowledge support from the Microbial Community Analysis and Functional Evaluation in Soils Program at Lawrence Berkeley National Laboratory for the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under contract DE-AC02-05CH11231 and award DE-SC0014079 to the University of California Berkeley. D. Newman thanks the ARO (W911NF-17-1-0024) and NIH (1R01AI127850-01A1) for support. Research in K. Zengler’s laboratory was supported in part by the National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health under award AR071731. Material is also based upon work supported by the National Science Foundation under grant 1332344 and the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research awards DE-SC0012586, DE-SC0012658, and DE-SC0018344 to K. Zengler. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Funding AgencyGrant Number
Department of Energy (DOE)DE-AC02-05CH11231
Department of Energy (DOE)DE-SC0014079
Army Research Office (ARO)W911NF-17-1-0024
Department of Energy (DOE)DE-SC0012586
Department of Energy (DOE)DE-SC0012658
Department of Energy (DOE)DE-SC0018344
Issue or Number:4
PubMed Central ID:PMC6050955
Record Number:CaltechAUTHORS:20180723-080501925
Persistent URL:
Official Citation:Zhalnina K, Zengler K, Newman D, Northen TR. 2018. Need for laboratory ecosystems to unravel the structures and functions of soil microbial communities mediated by chemistry. mBio 9:e01175-18.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:88114
Deposited By: Donna Wrublewski
Deposited On:23 Jul 2018 16:29
Last Modified:03 Oct 2019 20:03

Repository Staff Only: item control page