Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability - Fig 5

Spatial dynamics for (a) low and (b) high diffusion rates. (a) A low diffusion rate (D = 0.5) reduces the protective effect of the antibiotic (orange shading, lower panels), and the parasitic strain (black shading, upper panels) can invade the beneficial strain (yellow shading, upper panels). (b) A high diffusion rate (D = 50) allows the beneficial strain to resist invasion, as considerable amount of antibiotic (lower panels) diffuses beyond the colony boundaries. Antibiotic concentration ranges between zero (white), to intermediate (red-orange), to maximal concentrations (brown-black). Poisoned (cells with rPκ = 300 time steps to grow before invasion. The snapshots of the simulations are taken every 500 update steps. Model parameters are: rB,0 = 0.8, rP,0 = 0.8, c = 0.4, ρB,0 = 1, αB = 0.5, αP = 0.5, βB = 0.4, βP = 0, γB = 0.4, γP = 0.4, φ = 0.25, a = 1, T = 1, k = 25, N = 10 000, nB,0 = 100, nP,t = 10, κ = 300, f = 0.01, Δt = 1/10, u = 100, ε = 0.01, r+ = 0, s+ = 0, ρ+ = 0, and τ = 0.</p

The effect of efflux rate, decay rate, and diffusion rate on the <i>MSC</i>.

At low diffusion rates (upper row), efflux rate limits the success, while at large diffusion rate (bottom row), colony size is the more limiting factor. From left to right (a→b, c→d) extracellular decay rate increases (φ = 0.7 and 0.9). From the top to the bottom (a→c, and b→d), diffusion rate increases (D = 0.5 and 12), respectively. Model parameters are: rB,0 = 0.8, rP,0 = 0.8, c = 0.1, ρB,0 = 1, αB = 0.6, αP = 0.6, βP = 0, γB = 0.3, γP = 0.3, a = 1, T = 1, k = 25, N = 10 000, nB,0 = 100, nP,t = 10, κ = 300, f = 0.01, Δt = 1/10, u = 100, ε = 0.01, r+ = 0, s+ = 0, ρ+ = 0, and τ = 0.</p

The Minimal Sustainable Colony size (<i>MSC</i>) (Invasion test 2).

Invasion is initiated when the beneficial-strain colony reaches a defined size (CSI) and continues until the habitat is fully colonized by either the beneficial or the parasitic strains. The MSC is represented by the orange-red border separating the yellow (B wins) and black (P wins) regions. From left to right (a→c, d→f, and g→i), the extracellular decay rate of the antibiotic φ increases (φ = 0.2,0.25,0.3). From top to bottom (a→g, b→h, and c→i), the efflux rate βB decreases (βB = 1,0.5,0). Simulations were run with 3 replicates for 100 000 generations, or until the population was homogenous. Black areas indicate parameter space where the parasitic strain can invade, yellow indicates parameter space where the antibiotic-producing beneficial strain successfully resists invasion, and orange areas correspond to mixed outcomes. Model parameters are: rB,0 = 0.8, rP,0 = 0.8, c = 0.4, ρB,0 = 1, αB = 0.5, αP = 0.5, βP = 0, γB = 0.4, γP = 0.4, D = 5, a = 1, T = 1, k = 25, N = 10 000, nB,0 = 100, nP,t = 10, κ = 1, f = 0.01, Δt = 1/10, u = 100, ε = 0.01, r+ = 0, s+ = 0, ρ+ = 0, and τ = 0.</p

The effect of a private resource supplied by the host for a limited time <i>τ</i> (Invasion test 1).

Black areas indicate parameter space where the non-producing parasitic strain can invade, and the yellow shading indicates that the beneficial strain is able to resist invasion. Orange to red colours indicate mixed outcomes. In general, the beneficial strain dominates over a larger proportion of the parameter space as the duration of the private resource supply lengthens, regardless of whether the beneficial strain enjoys outright protected growth (a, b), an increased rate of population growth (c, d), or an increased rate of antibiotic production (e, f). The efflux of accumulated intracellular antibiotic in the antibiotic-producing beneficial strain also aids beneficial-strain dominance (βB = 0 for a, c, e, and βB = 0.25 for b, d, f). Simulations were run with 5 replicates for 100 000 generations or until the population was homogenous. Model parameters are: rB,0 = 0.8, rP,0 = 0.8, c = 0.1, ρB,0 = 1, αB = 0.5, αP = 0.5, βP = 0, γB = 0.4, γP = 0.4, φ = 0.3, D = 5, a = 1, T = 1, k = 25, N = 10 000, nB,0 = 100, nP,t = 10, κ = 1 f = 0.01, Δt = 1/10, u = 100, ε = 0.01, and r+ = 0, s+ = 0, ρ+ = 0 when applicable.</p

Model schematics.

(a) We model two strain types, parasitic (violet shading) and antibiotic-producer (blue shading), which compete with each other directly (grey arrow), and indirectly via the diffusing antibiotic (red dots and coloured arrows). (b) The modelled N = M*M grid (bottom layer) represents the colonisable surface of the host, and each point in the grid can be inhabited by a single individual (coloured quadrant). The produced antibiotic (upper layer) diffuses freely on the grid, and its concentration decreases farther from the producing source (the shading and height depicting the concentration) and also decays with time. (c) The growth dynamic of a colony follows a logistic trend in the model. We show the relative colony size (y-axis) with respect to time (x-axis) with ε = 1 (light blue), ε = 0.1 (medium blue), and ε = 0.01 (dark blue), where ε is the fraction of randomly chosen grid cells that is updated in the cellular reproduction and death processes. The smaller the ε, the slower the growth in our model. Relevant model parameters are: D = 5, Δt = 1/10, u = 100, for a nB,0 = 100, N = 10 000, and for b nB,0 = 1, M = 40, ρ= 1, αB = 0.5, βB = 0.6, γB = 0.3, φ = 0.5.</p

Sequence data

Raw 454 sequencing dat

PyroCleaning results for mtDNA COI amplicons generated from community samples of Collembola from two forest sites on the island of Tenerife.

<p>Each site has been amplified in triplicate. 62,825 raw reads were generated on 1/2 of a 454 plate from a total of 103,850 raw reads (the remainder of raw reads belonged to another experiment). Raw reads had a maximum length of 521 bp and an average length of 343 bp. Steps 3–6 are summarised in the text. Numbers in brackets represents sequence reduction as the % of raw reads above a minimum length of 170 nucleotides.</p

PyroCleaning results for mtDNA COI amplicons generated from experimental pools constructed from 27 genomic extracts from 23 Collembola species.

<p>Each pool has been amplified in triplicate. Sequences were generated on 1/2 a 454 plate that generated a total of 156,315 raw reads. Raw reads had a maximum length of 534 bp and an average length of 343.4 bp. Steps 3–4 are summarised in the text. Numbers in brackets represents sequence reduction as the % of raw reads above a minimum length of 170 nucleotides.</p

S1 fungus_CROP_R_script_nonrarefied

The HTML outputs of the R scripts using the non-rarefied CROP dataset

Datasets

This .zip files contains two folders. The folder "Control" contains the 15 raw 454 sequence files generated from the "Test Pools" analysis detailed in Table 2 of the manuscript, and a file of 27 Sanger sequences listed in Table S1. The folder "Tenerife" contains the 6 raw 454 sequence files associated generated from the "Tenerife Forest Samples" analysis detailed in Table 3 of the manuscript