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Legend for movies

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posted on 2012-06-14, 17:36 authored by Henry FolseHenry Folse

This file gives the legend for the movies, indicating which colors represent which genotypes of bacteria. Each type is given a three letter name with the letters C, N, and P, representing the enzymes for Carbon, Nitrogen, and Phosphorus. A capital letter represents the ability to make the enzyme, and a lower case letter represents the absence of this ability. For example, type CnP (pink) makes Carbon and Phosphorus enzymes, but not Nitrogen.

General Description

These animations show the evolution of a community of microbes, in silica representations of the bacteria that break down organic matter in the soil. The entire grid is only 100 microns (0.1 mm) across, and each pixel represents 1 micron (10-6 m). These microbes secrete digestive enzymes similar to the ones produced in the human stomach, which break down the large macromolecules of nutrients in the soil into tiny monomers, which can be taken into the cell. Once outside the cell, these enzymes will disperse away from the microbe that produced them by passive diffusion, and neighboring microbes will be able to take advantage of their effects as well. For this reason, these enzymes are considered a public good, a term borrowed from economics that means any product that freely benefits an entire community and not just the producer of the good. The production of public goods is a classic example of cooperation. However, public goods are also subject to cheating by freeloaders, individuals who take advantage of the benefits of the good, but do not contribute. If the burden of cheaters becomes too high, it can cause an entire community to collapse in extinction.

In these simulations, there are three nutrients, Carbon (C), Nitrogen, (N), and Phosphorous (P), each of which is necessary for survival and reproduction, each an independent public good. Each colored pixel represents an individual microbe, and the color symbolizes its genotype. Hotter colors represent types that produce more enzymes. Red is the hottest, the only one that produces all three enzymes, and so is completely self-sufficient. Blue is the coolest, the only one that produces no enzymes, a pure freeloader. Orange, yellow, pink, light blue, green, and purple all represent intermediate genotypes, which produce some enzymes but not others. They cannot survive alone, but mutually catalyze each other’s growth, and can compete successfully in coalition with each other. Two coalitions that are particularly successful are orange-purple and pink-green.

At the beginning of each simulation, there is an explosion of growth, a fireworks display of color representing the initial diversity of the community. As time goes on, the blue freeloaders put a heavier burden on the community, causing the population to decline. As it declines, it goes through a bottleneck, a period of very low population size, in which much of the diversity is lost. Only a few types will survive, and the types that do are largely random. After the bottleneck, resources are scarce for cheaters. Their dependence on producers means they lack self-sufficiency. With no one to exploit, they begin to die. Once the pressure of the cheaters is relaxed, the population recovers, but with reduced diversity. Sometimes the red producers survive, cycling back and forth with the blue cheaters. Other times it is a two-way coalition, orange and purple or pink and green. Other times still it is a three-way coalition of light-blue, green, and purple. Notice how the different types form different shapes. Red producers form huge, dense, aggregations. Blue cheaters are more spread out, clinging to the edges of the producer colonies they depend on. Intermediate types form other shapes as they meander across the grid. These spatial patterns are not coded into the simulation, but emerge spontaneously as a result of the interplay of cooperative and competitive interactions between microbes of the same and different types. 

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