no allelopathy model data

Species abundance and resource use data from model runs with various levels of gamma

allelopathy model data

Species abundance, resource use and antimicrobial production data from model runs with various levels of gamma

script for both models with annotation

R script for models

Isolate and community local adaptation

Isolate and community local adaptation at day 81 of experimental evolution

community growth and diversity during evolution experiment

Microbial community growth rates (total change in OD600 over 24 to 96 hours) measured in triplicate at two assay temperatures every 9 days for 81 days. Shannon diversity and community evenness are both calculated for experimental blocks 1, 3 and 5 from samples taken on days 27, 54 and 81. Time is reported in hours. Temperature reported in degrees Celsius

biolog metabolism data during evolution experiment

Community carbohydrate use during experimental evolution. Carbohydrate use (with threshold of OD600 > 0.2) for starting community and across sampling days 27, 54 and 81 and change in carbohydrate use. Column, biologcarb, refers to the carbohydrate at that well position on biolog GN2 microplate

The interspecific impacts of resource use on relative growth.

<p>Interspecific effect on relative growth among species inferred from their ability to grow on sterile beech tea previously used by each other species, shown separately for each treatment. Blue arrows indicate negative effects on growth, and red arrows indicate positive effects on growth. The width of the arrow represents the maximum growth rate (<i>V_MAX</i>) on used tea minus the maximum growth rate on unused tea (underlying data in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001330#pbio.1001330.s001" target="_blank">Figure S1</a> and linear model in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001330#pbio.1001330.s012" target="_blank">Table S4</a>). Dashed lines indicate that growth on used tea was not significantly different from growth on unused tea.</p

Correspondence between compounds being generated and compounds being used up by other species in polycultures.

<p>The data summarize results from assays growing one species on beech tea medium, filtering that medium, and then growing a second species on the used medium. We calculated two quantities: δ_0,1 = the amount of compound in the filtrate from species 1 minus the amount of compound in beech tea (relative to the amount of the DSS standard); δ_1,2 = the amount of compound in the filtrate from species 2 minus the amount of compound in filtrate from species 1. Positive δ indicates production of compounds during the assay and negative δ indicates consumption. We then compared δ between evolved and ancestral isolates for different species pairs: each point shows the comparison for a given species pair and either monoculture (black circles) or polyculture (grey crosses) treatments. The <i>x</i>-axis is δ_0,1 of the evolved isolate minus δ_0,1 of the corresponding ancestral isolate. More positive values indicate that the evolved isolate of the first species produced more of that compound than did its ancestral isolate. To focus on waste products as potential targets of cross-feeding, only compounds that were produced by the evolved isolate were included. The <i>y</i>-axis is δ_1,2 for evolved isolate minus δ_1,2 for the corresponding ancestral isolate. More negative values indicate that the evolved isolate of the second species used more of the compound than did its ancestral isolate. For example, the point indicated by the arrow represents increased production of acetate by species A in polyculture relative to ancestral isolates (<i>x</i>-axis) and its increased use by species D in polyculture relative to ancestral isolates (<i>y</i>-axis, all changes shown separately by species and compound in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001330#pbio.1001330.s005" target="_blank">Figure S5</a>). There is a general negative trend: if the first species produces more of a compound, the second species is likely to use more of it. However, the effect is significantly stronger in polyculture isolates (grey dashed line) than in monocultures (black line): polyculture isolates have evolved increased consumption of compounds that have increased in production in polyculture isolates of other species. Linear model of y = x * treatment (monoculture or polyculture), interaction term coefficient = −1.13, <i>t</i> = −5.4, <i>p</i><0.0001.</p

Maximum growth rates of isolates after evolution under each diversity treatment.

<p>Maximum rate of growth from low densities, <i>V_MAX</i>, of each species grown on unused beech tea under assay conditions. Dark bars, growth rates of ancestral isolates. Mid grey bars, growth rates of monoculture isolates. Pale bars, growth rates of polyculture isolates. Standard error bars are shown. Tukey Honest Significant Difference test contrasts between treatments: *** <i>p</i><0.001, ** <i>p</i><0.01, * <i>p</i><0.05; n.s., not significant (see also <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001330#pbio.1001330.s012" target="_blank">Table S4</a>). Species A evolved slower maximum growth rates in polycultures compared to its ancestral and monoculture isolates. Species B and C evolved faster maximum growth rates on unused beech tea in monocultures, but far slower maximum growth rates in polycultures compared to ancestral isolates. Species D evolved faster maximum growth rates in monocultures compared to its ancestral isolate and even faster maximum growth rates in polycultures.</p

Experimental design for the evolution experiments.

<p>(i) Stocks of wild isolates were grown up, each comprising a single starting genotype of each species. (ii) Experiments were started with each species in monoculture or in polyculture (all five species mixed together). (iii) To stimulate active growth and promote adaptation to the laboratory conditions, each culture was diluted 20-fold in fresh medium twice weekly for 8 wk. Tubes were shaken to prevent the formation of biofilms and maintain spatial homogeneity. Numbers of generations ranged from 60.9 to 82.2 across cultures and effective population sizes ranged from 5.3×10⁵ to 9.9×10⁶ (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001330#pbio.1001330.s011" target="_blank">Table S3</a>). (iv) Final cultures were plated on agar. (v) Single colonies of each species were isolated for growth assays described in the main text.</p