Fig 1.
Classification of eco-interactions between species.
Cross-feeding (or syntrophy) and co-protection (or symprostasy) are two specific eco-interactions belonging to mutualism (positive effect for both interacting species).
Table 1.
Definition of eco-interactions.
Summary of ecological net effect on bacteria and their respective metabolic stoichiometries.
Fig 2.
Spatial distribution of microbial populations at different substrates concentrations.
(A) Aggregate pictures captured after 8 d of simulation considering neutralism, competition and commensalism with [S]T = 100 mM. (B) Aggregate pictures captured at 10 d of simulation considering neutralism, competition and commensalism with [S]T = 10 mM. (C) Aggregate pictures captured at 15 d of simulation considering neutralism, competition and commensalism with [S]T = 1 mM. None of the simulations are in steady state yet. Black solid line on bottom-right of aggregates represent the scale bar. Substrate profiles on the transverse plane of aggregates have been included on S2 Fig.
Fig 3.
(A) Relative abundances of B1, B2 and B3 populations in the community. Dashed red lines indicate 33.33% and 66.66% relative abundances. (B) Microbial fitness (median, ) is calculated in all replicates (n = 3 for 1.0 mM and 0.5 mM, n = 6 for 0.2 mM). Asterisks indicate the significance level of the difference between B1, B2 and B3 specific growth rate. (C) Aggregates captured at steady state (75 d for 1.0 mM and 0.5 mM, 100 d for 0.2 mM). Inactive bacteria are shown in a lighter colour. Black solid lines on bottom represent the scale bars. Significance level legend: ns, not significant; *, p < 0.05; **, p < 0.01; ***, p < 0.001.
Fig 4.
(A) Relative abundances of B1, B2 and B3 populations in the community. Dashed red lines indicate 33.33% and 66.66% relative abundances. (B) Microbial fitness (median, ) is calculated in all replicates (n = 3 for 1.0 mM and 0.5 mM; n = 6 for 0.2 mM and 0.1 mM). Asterisks indicate the significance level of the difference between the specific growth rate of B1, B2 and B3 populations. (C) Aggregates captured at steady state (50 d for 1.0 mM and 0.5 mM, 75 d for 0.2 mM and 0.1 mM). Inactive bacteria are shown in a lighter colour. Black solid lines on bottom represent the scale bars. (D) Average relative size of colonies (with respect to the total perimeter of the aggregate) is calculated in all replicates (n = 3 for 1.0 mM and 0.5 mM; n = 6 for 0.2 mM and 0.1 mM). Asterisks indicate the significance level of the difference between substrates concentrations. Significance level legend: ns, not significant; *, p < 0.05; **, p < 0.01; ***, p < 0.001.
Fig 5.
(A) Relative abundances of B1, B2 and B3 populations in the community. Dashed red lines indicate 33.33% and 66.66% relative abundances. Square brackets with asterisks indicate the significance level of the difference between relative abundances between populations. Colour of asterisks points out what bacteria it refers to. (B) Microbial fitness (median, ) is calculated in all replicates (n = 3 for 1.0 mM and 0.5 mM; n = 6 for 0.2 mM and 0.1 mM). (C) Aggregates captured at steady state (50 d for 1.0 mM and 0.5 mM, 75 d for 0.2 mM and 0.1 mM). Inactive bacteria are shown in a lighter colour. Black solid lines on bottom represent the scale bars. (D) Transient change of growth rate ratios of active B2 and B3 over B1 (
and
, respectively) in all replicates (n = 3 for 1.0 mM and 0.5 mM; n = 6 for 0.2 mM and 0.1 mM). Growth rate ratios, normalise the comparison and reduce the influence of substrate concentration in the analysis. Dimensionless time was applied to compare simulations with different time length (tmax). Asterisks indicate the significance level of difference between 1.0 mM and the other concentrations (1.0 mM vs 0.5 mM; 1.0 mM vs 0.2 mM; 1.0 mM vs 0.1 mM). Colour of asterisks: red–growth rate ratio at [S] is lower than that at 1.0 mM; blue–growth rate ratio at [S] is higher than that at 1.0 mM. Significance level legend: ns, not significant; *, p < 0.05; **, p < 0.01; ***, p < 0.001. Width of the lines indicate the time to which the significance level corresponds. Colour of the lines: green–B2; orange–B3.
Fig 6.
Aggregates captured at steady state considering commensalism and competition for O2.
Steady state times: 50d for [S]T = 1.0 mM, 0.5 mM, 0.1 mM and [O]2 = 10 mg/L, 6 mg/L; 75d for [S]T = 1.0 mM, 0.5 mM, 0.1 mM and [O]2 = 1 mg/L; 100d for [S]T = 0.05 mM and [O]2 = 10 mg/L, 6 mg/L, 1 mg/L. Inactive bacteria are shown in a lighter colour. Substrate profiles on the transverse plane of aggregates have been included on S5 Fig. Aggregates captured at steady state.
Fig 7.
Eco-interaction modulus diagram for simulations considering commensalism and competition for O2 with [A] = 1.0–0.1 mM and [O2] = 14–1 mg/L.
Aggregates captured at steady state (75 d for [S]T = 1.0 mM and [O2] = 1 mg/L; 50 d for all other conditions). Inactive bacteria are shown in a lighter colour. Eco-interaction modulus calculated by Eq 1 for each replicate. Colour legend: B1 –purple; B2 –green; B3 –orange.
Fig 8.
Influence of shear force (detachment) to spatial distribution of microbial populations.
A maximum radius of 30 μm was set when detachment was considered. Aggregates captured at 50 d. Three conditions were evaluated–competition ([S]T = 0.2 mM), commensalism ([S]T = 0.1 mM), and commensalism + competition ([S]T = 0.1 mM and [O2] = 10 mg/L). Inactive bacteria are shown in a lighter colour. Substrate profiles on the transverse plane of aggregates have been included on S11 Fig. The simulation experiments including detachment were started with the same inoculum as those without detachment with the objective to observe the genuine impact of the shear force in the spatial distribution of the microbial populations.
Fig 9.
Individual-based Model description.
(A) Representation of simulation domain. An expansion of specific aggregate zone (bottom-right square), and an example of the initial distribution of cells (top-right square) are shown, where microbes are represented as coloured circles with a specific radius: B1 –purple circle; B2 –green circle; B3 –orange circle. (B) Hypothetical position of microbes in the node. Only “microbe A” belongs to node i,j because its centre is inside the node. (C) Microbial division and inactivation. α is any stochastic value between 0.45–0.55. Mmax and Mmin refer to the maximum and minimum mass that microbe can reach, respectively.
Fig 10.
Representation of eco-interactions among B1 (purple), B2 (green) and B3 (orange).
(A) Neutralism: [0,0,0]; no impact on B1, B2 and B3. (B) Competition: [–,–,–]; negative impact on B1, B2 and B3. (C) Commensalism: [0,+,+]; no impact on B1, positive impact on B2 and B3. (D) Commensalism + competition: [0,+,+] or [–,–,–]; impact on B1, B2 and B3 is defined by the environment.