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Title: Species interactions differ in their genetic robustness

Abstract

Conflict and cooperation between bacterial species drive the composition and function of microbial communities. Stability of these emergent properties will be influenced by the degree to which species' interactions are robust to genetic perturbations. We use genome-scale metabolic modeling to computationally analyze the impact of genetic changes when Escherichia coli and Salmonella enterica compete, or cooperate. We systematically knocked out in silico each reaction in the metabolic network of E. coli to construct all 2583 mutant stoichiometric models. Then, using a recently developed multi-scale computational framework, we simulated the growth of each mutant E. coli in the presence of S. enterica. The type of interaction between species was set by modulating the initial metabolites present in the environment. We found that the community was most robust to genetic perturbations when the organisms were cooperating. Species ratios were more stable in the cooperative community, and community biomass had equal variance in the two contexts. Additionally, the number of mutations that have a substantial effect is lower when the species cooperate than when they are competing. In contrast, when mutations were added to the S. enterica network the system was more robust when the bacteria were competing. These results highlight the utilitymore » of connecting metabolic mechanisms and studies of ecological stability. Cooperation and conflict alter the connection between genetic changes and properties that emerge at higher levels of biological organization.« less

Authors:
 [1];  [2];  [2];  [3]
  1. Univ. of Missouri - St. Louis, MO (United States). Dept. of Biology
  2. Boston Univ., MA (United States). Bioinformatics Program
  3. Univ. of Minnesota, St. Paul, MN (United States). Dept. of Ecology, Evolution, and Behavior and BioTechnology Inst.
Publication Date:
Research Org.:
Boston Univ., MA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Institutes of Health (NIH)
OSTI Identifier:
1185123
Grant/Contract Number:  
SC0004962
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 6; Journal Issue: C; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; cooperation; competition; genetic robustness; E. coli; Salmonella; community stability; metabolic modeling

Citation Formats

Chubiz, Lon M., Granger, Brian R., Segre, Daniel, and Harcombe, William R. Species interactions differ in their genetic robustness. United States: N. p., 2015. Web. doi:10.3389/fmicb.2015.00271.
Chubiz, Lon M., Granger, Brian R., Segre, Daniel, & Harcombe, William R. Species interactions differ in their genetic robustness. United States. doi:10.3389/fmicb.2015.00271.
Chubiz, Lon M., Granger, Brian R., Segre, Daniel, and Harcombe, William R. Tue . "Species interactions differ in their genetic robustness". United States. doi:10.3389/fmicb.2015.00271. https://www.osti.gov/servlets/purl/1185123.
@article{osti_1185123,
title = {Species interactions differ in their genetic robustness},
author = {Chubiz, Lon M. and Granger, Brian R. and Segre, Daniel and Harcombe, William R.},
abstractNote = {Conflict and cooperation between bacterial species drive the composition and function of microbial communities. Stability of these emergent properties will be influenced by the degree to which species' interactions are robust to genetic perturbations. We use genome-scale metabolic modeling to computationally analyze the impact of genetic changes when Escherichia coli and Salmonella enterica compete, or cooperate. We systematically knocked out in silico each reaction in the metabolic network of E. coli to construct all 2583 mutant stoichiometric models. Then, using a recently developed multi-scale computational framework, we simulated the growth of each mutant E. coli in the presence of S. enterica. The type of interaction between species was set by modulating the initial metabolites present in the environment. We found that the community was most robust to genetic perturbations when the organisms were cooperating. Species ratios were more stable in the cooperative community, and community biomass had equal variance in the two contexts. Additionally, the number of mutations that have a substantial effect is lower when the species cooperate than when they are competing. In contrast, when mutations were added to the S. enterica network the system was more robust when the bacteria were competing. These results highlight the utility of connecting metabolic mechanisms and studies of ecological stability. Cooperation and conflict alter the connection between genetic changes and properties that emerge at higher levels of biological organization.},
doi = {10.3389/fmicb.2015.00271},
journal = {Frontiers in Microbiology},
number = C,
volume = 6,
place = {United States},
year = {2015},
month = {4}
}

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