projectProposal

For my project I am interested in modeling microbial community structure and the formation of stable communities from a random assortment of species. One of the underlying principles of microbial biogeography and ecology is “everything is everywhere and the environment selects.” This is the idea that most microorganisms are present in all environments but the ones that thrive are determined by the environment. I am interested in exploring this idea by trying to understand how different stable communities can form. This can be thought of as a fitness landscape of entire communities rather than an individual organism, where the fitness peaks are groups of species that are stable and the valleys are transitional states. 
There exist many general ecological models and while many of the same underlying principles apply to microbial communities modeling these communities is different because there are key differences between the lifestyles of microbes and multicellular organisms. Key differences include:
•   Microbes are highly dependent on one another
•   They form gilds that are separate from species. Guild members do the same thing ecologically but evolve differently and have different nutritional requirements
•   They engage in a wide variety of "social" interactions such as mutualism, commensalism, parasitism etc.
•   Communities are not uniform. Bacteria are so small that there are micro niches within something as small as a soil particle where two very different microbes can live.
One of the major challenges I see in modeling a microbial community is the number of agents. In natural communities there can be upwards of billions of individuals doing any number of different things. In my project I propose to abstract this and focus on community structure and stability, having species and guilds acting as “super agents.” On the surface my model will have three main events: communities are allowed to assemble, a perturbation will disrupt the community and the communities will then be allowed to reassemble. 
Things to look for in the model:
•   Are the communities that form stable?
•   Do the same members return after perturbations?
•   Do the same guilds return?
•   Is the succession order the same?
•   Does a stable community evolve over time or is it unchanging from the beginning?
Each organism is an agent and falls into two categories, species and guild. A species is a biological species i.e. all members of the species share the same "genome" in that they have the same metabolism and nutrient requirements. A guild is a group of organisms that perform the same ecological function, so they may have the same metabolism but they may not all share the same resource requirements. Losing one species in a guild will not remove the ecological function in the environment, but it will be reduced.
The environment where the organisms live has a list of resources in varying abundances. The resources are edibles, breathables, and nutrients. Each organism requires an edible, a breathable, macronutrients and micronutrients and creates byproducts in the environment. These byproducts may be nutrients for other organisms. The guilds are groups of organisms that produce the same byproducts. Each organism has a combination of edibles and breathables collectively called metabolism and each of these combinations are ranked from best to worst. All organisms compete for six nutrients needed in high abundance, which are carbon, hydrogen, nitrogen, oxygen, phosphate and sulfur. Other nutrients are present in the environment and are required in varying amounts by each organism, these are the micronutrients. All organisms produce a byproduct determined by their metabolism.
The environment will be a score sheet of available resources. Perturbations will change the level of resources that are available in the environment. All organisms will get a shot colonization of the environment after a perturbation but they must compete with the community that was present before the perturbation.
The organisms with the highest score (determined by metabolism) will get the most resources. They will try to maximize their score and resource consumption. All organisms get a shot at living in the environment at the start (this is the idea that everything is everywhere). They may not appear at first, these will be considered the low abundance organisms, but they may appear at larger numbers if the colonizing organisms change the landscape of the environment through their metabolism. For example, at the beginning of the experiment there may not be a resource available for a particular species, but another species may produce this resource as a byproduct. The low abundance species may be able to colonize the environment after enough of this resource has accumulated. Score determines reproduction; higher scoring organisms will reproduce more often than the lower scoring organisms. An organism dies when it doesn’t have enough resources or it reaches a certain age. It is then removed from the environment and the resources it consumed in its lifetime are returned to the environment.
At each timestep each species checks to see if it can enter the environment. If it can't, it waits until the next turn otherwise it enters and gathers nutrients according to its metabolism score. This may cause some organisms to take over the environment and thus change the resource availability. The waiting species then check on the next turn to see if they can now enter the environment (step 1).  Resources are replenished only when an organism produces the resource as a byproduct or dies. This process repeats until a perturbation happens, which changes the resource abundance. The community is not reset after this perturbation, rather the organisms that are living there must continue to try to make a living or a new organism may enter the community.
Possible enhancement: at random times a mutation may occur that changes the resource requirements of an organism.
I plan to use Python and Simpy for the project.