Figure 4. Directed evolution produces communities that are resistant to ecological perturbations.

(A) We compare the function and ecological stability of communities engineered from the top-down by directed evolution (DE; red), with a synthetic bottom-up consortium (purple). A no-selection (NS; green) control is also provided for reference. The DE community was found by multiple rounds of selection using a protocol that combines bottleneck and migration to generate variants. The synthetic community of equal diversity (species richness) was assembled by mixing together high-ϕ_i species from the regional pool (Methods). The top community of the NS control was also chosen as reference. (B) The three communities were stabilized for 20 generations (note that the DE and NS were already in equilibrium at the start, but the synthetic community was not). After that, each community was subject to invasion by a randomly sampled set of species from the regional species pool (Methods). This process was repeated 95 independent times for each community. The perturbed communities (lighter-color lines) were allowed to equilibrate by passaging for an additional 20 generations without artificial selection. Following the perturbation, communities reached a new state with function F*, and from the changes in function before and after the perturbation we compute the resistance R (inset equation) ⁸⁰. (C-D) The values of F* and R resulting from panel (B) are plotted. Values above brackets represent p-values of paired t-tests (N = 95 each test). (E-F) The experiment in (B) was repeated 100 times with as many different initial DE, NS, and synthetic consortia. (E) shows F_max of 100 independent experiments. Values above brackets represent p-values of two-sided paired t-tests (N=100 each test) (F) Mean(R) vs Mean(F*) for all 100 independent experiments. *:p<0.05, ****:p<0.0001.