Fig 1.
Evolved communities of E. coli and S. Typhimurium are more efficient in resource utilization.
(A) A depiction of the two-species synthetic microbial community of E. coli and S. Typhimurium used in the study. There is significant resource usage overlap between E. coli and S. Typhimurium in nutrient-rich LB media, suggesting strong interspecies and intraspecies resource competition. (B) Coexistence and steady state were determined in the synthetic two-species community by performing invasion experiments using different starting frequencies of E. coli: S. Typhimurium (ranging from 1:99 to 99:1). Eight replicates were used in each case. The Y-axis represents natural log-transformed values for the ratios between E. coli and S. Typhimurium. The data underlying this figure can be found in S1 Data, in the sheet titled Fig 1B. (C) Clones of E. coli and S. Typhimurium that were isolated from the evolved communities showed increased fitness when competed against the respective ancestors. The Y-axis represents the selection coefficient calculated by competing the evolved clones with the respective ancestral strains. Four replicates were used in each case, and the line in the center represents the median value. The data underlying this figure can be found in S1 Data, in the sheet titled Fig 1C. (D) Mutations identified by performing whole-genome sequencing analysis of evolved E. coli and S. Typhimurium clones. Five clones isolated from different communities were whole-genome sequenced for each species. Different mutations occurring in the same clone are denoted by the same color of the gene label.
Fig 2.
Evolved communities of E. coli and S. Typhimurium are less resistant to invasion.
(A) Schematic representation of experiments performed to determine invasion resistance of ancestral and evolved communities of E. coli and S. Typhimurium against a colicin-producing E. coli. Evolved communities were formed by mixing 10 evolved E. coli and S. Typhimurium clones that were isolated from the same evolving community. (B) Invasion resistance was determined by measuring selection coefficients in competition experiments between colicin-producing E. coli and susceptible E. coli in ancestral and evolved communities. Eight replicates were used in each case and the line in the center represents the median value. The X-axis represents the ancestral and evolved communities and the Y-axis represents the selection coefficients showing the change in frequency of the colicin-producing E. coli with respect to the susceptible E. coli. A Student’s t test (with Bonferroni’s correction for multiple testing) was performed to determine statistically significant differences (denoted as * for p < 0.05) between the ancestral and each of the evolved states. The numbers on the X-axis represent the strain IDs for ancestral and evolved clones of E. coli and S. Typhimurium used in the study. The data underlying this figure can be found in S1 Data, in the sheet titled Fig 2B.
Fig 3.
Two-way competitions reveal heightened interspecific competition and ecological specialization in the evolved communities.
Two-way species interactions were determined by measuring selection coefficients for two-way competition experiments between (A) colicin-producing E. coli and susceptible E. coli, (B) colicin-producing E. coli and S. Typhimurium, and (C) cognate pairs of E. coli and S. Typhimurium. Eight replicates were used in each case and the line in the center represents the median value. In each case, ancestral clones are denoted as Anc and evolved clones are denoted as Evo. The X-axis represents the ancestral and evolved clones/communities and the Y-axis represents the selection coefficients showing the change in frequency of the first species with respect to the second species. A Student’s t test (with Bonferroni’s correction for multiple testing) was performed to determine statistically significant differences (denoted as * for p < 0.05) between the ancestral and each of the evolved states. The numbers on the X-axis represent the strain IDs for ancestral and evolved clones of E. coli and S. Typhimurium used in the study. The data underlying this figure can be found in S1 Data, in the sheet titled Fig 3.
Fig 4.
Lotka–Volterra interspecific competition model corroborates the link between interspecific competition and invasion success.
Outcomes based on a three-species Lotka–Volterra interspecific competition model that was extended to include killing by toxin (Materials and methods). In this model, the strength of interspecies interactions and the degree of ecological specialization are varied by adjusting the two-way competition coefficients. Specifically, the effect of S. Typhimurium on the growth of susceptible E. coli (representing the strength of interspecies interaction) and colicin-producing E. coli (representing ecological specialization) is modified by changing the competition coefficient aES and aCS, respectively. The effect of colicin-producing E. coli on the growth of the susceptible E. coli, due to competition for resources, is varied by changing aEC (represented as different colors in the figure). X-axis represents the strength of interspecies interaction and is calculated as the ratio between aES/aEE (Materials and methods). The selection coefficient represents the outcome of competition between the colicin-producing E. coli and susceptible E. coli in 3 species communities computed by numerically solving the model and is the measure of the invasion rate of the colicin-producing E. coli. A dependence of this invasion rate on the strength of interspecies interaction and ecological specialization is observed.
Fig 5.
An increase in resource competition within a community results in a decrease in invasion resistance.
A schematic representation of the interplay between resource competition and invasion resistance in microbial communities. As the strength of resource competition increases within the community, the resistance to a toxin-producing invader reduces. Furthermore, these invasion dynamics are not predictable based on two-way competition outcomes between the community members and the invader.