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Title: Design of synthetic bacterial communities for predictable plant phenotypes

Abstract

Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant–bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation–responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. In conclusion, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities.

Authors:
 [1];  [2];  [3];  [3];  [3];  [3];  [3];  [4];  [5];  [3];  [3];  [6];  [3];  [7];  [8]
  1. Univ. of North Carolina, Chapel Hill, NC (United States); Stanford Univ., Stanford, CA (United States)
  2. Univ. of North Carolina, Chapel Hill, NC (United States); Facebook Inc., Seattle, WA (United States)
  3. Univ. of North Carolina, Chapel Hill, NC (United States)
  4. Univ. of North Carolina, Chapel Hill, NC (United States); BD Technologies, Durham, NC (United States)
  5. Univ. of North Carolina, Chapel Hill, NC (United States); Univ. of Georgia, Athens, GA (United States)
  6. Univ. of North Carolina, Chapel Hill, NC (United States); Calico Life Sciences, San Francisco, CA (United States)
  7. Univ. of North Carolina, Chapel Hill, NC (United States); Univ. of Nottingham, Sutton Bonington (United Kingdom)
  8. Max Planck Inst., Heidelberg (Germany)
Publication Date:
Research Org.:
Univ. of Nebraska, Lincoln, NE (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1499872
Grant/Contract Number:  
SC0014395
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS biology (Online)
Additional Journal Information:
Journal Volume: 16; Journal Issue: 2; Journal ID: ISSN 1545-7885
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Herrera Paredes, Sur, Gao, Tianxiang, Law, Theresa F., Finkel, Omri M., Mucyn, Tatiana, Teixeira, Paulo José Pereira Lima, Salas González, Isaí, Feltcher, Meghan E., Powers, Matthew J., Shank, Elizabeth A., Jones, Corbin D., Jojic, Vladimir, Dangl, Jeffery L., Castrillo, Gabriel, and Kemen, Eric. Design of synthetic bacterial communities for predictable plant phenotypes. United States: N. p., 2018. Web. doi:10.1371/journal.pbio.2003962.
Herrera Paredes, Sur, Gao, Tianxiang, Law, Theresa F., Finkel, Omri M., Mucyn, Tatiana, Teixeira, Paulo José Pereira Lima, Salas González, Isaí, Feltcher, Meghan E., Powers, Matthew J., Shank, Elizabeth A., Jones, Corbin D., Jojic, Vladimir, Dangl, Jeffery L., Castrillo, Gabriel, & Kemen, Eric. Design of synthetic bacterial communities for predictable plant phenotypes. United States. doi:10.1371/journal.pbio.2003962.
Herrera Paredes, Sur, Gao, Tianxiang, Law, Theresa F., Finkel, Omri M., Mucyn, Tatiana, Teixeira, Paulo José Pereira Lima, Salas González, Isaí, Feltcher, Meghan E., Powers, Matthew J., Shank, Elizabeth A., Jones, Corbin D., Jojic, Vladimir, Dangl, Jeffery L., Castrillo, Gabriel, and Kemen, Eric. Tue . "Design of synthetic bacterial communities for predictable plant phenotypes". United States. doi:10.1371/journal.pbio.2003962. https://www.osti.gov/servlets/purl/1499872.
@article{osti_1499872,
title = {Design of synthetic bacterial communities for predictable plant phenotypes},
author = {Herrera Paredes, Sur and Gao, Tianxiang and Law, Theresa F. and Finkel, Omri M. and Mucyn, Tatiana and Teixeira, Paulo José Pereira Lima and Salas González, Isaí and Feltcher, Meghan E. and Powers, Matthew J. and Shank, Elizabeth A. and Jones, Corbin D. and Jojic, Vladimir and Dangl, Jeffery L. and Castrillo, Gabriel and Kemen, Eric},
abstractNote = {Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant–bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation–responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. In conclusion, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities.},
doi = {10.1371/journal.pbio.2003962},
journal = {PLoS biology (Online)},
issn = {1545-7885},
number = 2,
volume = 16,
place = {United States},
year = {2018},
month = {2}
}

Journal Article:
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