Phage-bacteria coevolution

If you don't see a dynamic network like in the picture above, please install Java.

This applet simulates a coarse grained model of interactions between temperate phages (orange), virulent phages (red), and bacteria (black) on the strain level.

A bacterial strain is duplicated every time step. You can control the number of phage strains that are simultaneously duplicated by adjusting the associated scrollbars. There are two duplication modes. In the default “Constrained”, you set the exact number of virulent and temperate phage duplications, independent of relative number of strains. If “Free” is selected you can set the total number of phage duplications and the bias between the two different phages. A duplication event for any of the two phage types occurs proportional to the number of strains multiplied by the bias.

The weak load refers to genetic load per outgoing link from a phage and the load per link from a temperate phage on a bacterial strain. The strong load is associated to the load per link from a virulent phage on a bacterium. If a temperate phage has links to both a virulent phage and bacterial strain that are connected, then the bacterium is provided immunity from the temperate phage against the virulent phage (dashed link). The link between the virulent phage and the bacterium is therefore weak.

Bacteria and their phages are the most abundant, widespread and diverse groups of biological entities on the planet. There are about 5,000,000,000, 000,000,000, 000,000,000,000 bacteria on the planet, and even more phages. Bacteria govern large part of our ecosystem, and are believed to be responsible for 30-50% of the CO2 recycling in the atmosphere. Phages come in two major groups, the virulent ones and the temperate ones. A successful virulent phage always kills the infected bacteria, whereas a temperate phage often co-exist within the bacteria and provide immunity against a subsequent infection of some virulent phages.

In an attempt to understand how the highly dynamical and co-evolving system of bacteria and their predators govern itself we developed a stochastic network model. The model, which deals with bacteria, and the two distinct groups of predators represented by virulent and temperate phages.

The model is designed to pose questions related to diversity in these ecologies, and works with units that represent whole species or strains of bacteria or phages. Accordingly, nodes represent whole strains of bacteria or phages in the applet above rather than individuals, with “speciation” and extinction modeled by duplication and removal of nodes. Phage-bacterium links represent host-parasite relationships and temperate-virulent phage links denote prophage-encoded resistance. The effect of horizontal transfer of genetic information between neighbor strains in the network is also included in the dynamical rules, regulated by the global versus local scroll on the right panel.

The java applet have 4 key parameters, which we do not known for the real ecosystem. For all parameter sets, the observed networks evolve in a highly dynamic fashion with a topology that always varies greatly from time to time. Also, for all parameter sets, the ecosystems are prone to collapse (one or more entire groups go extinct), unless coexistence of all groups are maintained artificially by setting the probability of speciation within each group to be independent of its diversity (“Constrained”). This reflects the behavior of an ecosystem where speciation rates are primarily set by the availability of ecological niches.

Reference: M. Rosvall, I.B. Dodd, S. Krishna, and K. Sneppen, Network Models of Phage-Bacteria Co-evolution.