I am pleased to report that the Anabaena model paper is now published in Environmental Microbiology.
In this paper we present a dynamic, mechanistic, gene level model of Anabaena – nitrogen interaction. This model is unique and constitutes a significant step in the area of microbial ecology, where models are typically based on concepts developed over 50 years ago (i.e., Monod kinetics), do not include modern biology and do not make predictions commensurate with modern observational technologies (e.g., transcript levels). The model development process is also novel in the context of microbial ecology. It builds on a large database of empirical observations, data from 55 papers (269 experiments) were digitized and used for model-data comparison (i.e. a meta-analysis). The model helps to interpret the observations. For example, application to isotope tracing experiments suggests a role for an N storage pool, consistent with recent observations. We use the model to explore an important question about the efficacy of reducing nitrogen to control lake eutrophication. Beyond these results we propose that our approach constitutes a way to summarize observations that has significant advantages over the traditional review paper when the amount of observations is large. We believe this paper makes a significant contribution to the biology and ecology of Anabaena and presents a novel approach that is of interest to researchers in other areas of microbiology and ecology.
I want to use this post to lay out some of the thoughts I have about possible follow-on projects for this model. The overall “master plan” for the Anabaena model is shown in the figure below, and some more details follow. Please contact me, if you are interested in collaborating on any of these projects.
Anabaena Lab: This is done now. To give you some idea of the effort involved: The Anabaena Lab model took much of my time over the course of a year. I think on average about 4h/day.
Anabaena Lab Validation: This is a validation exercise. It would involve taking additional papers that were not used in the model development and comparing the model to those. The present model was developed and compared to experiments from 55 papers. This exercise may include about 10 papers. I already have these papers identified. This would be a good MS thesis project for a student. Along with this paper, I would like to publish the source code and user guide of the model as well.
Anabaena Field: The present model can be applied to a real lake. Since it only includes Anabaena, this lake would have to be dominated by Anabaena. If everything goes smoothly, this could also be a good MS thesis project.
Microcystis Toxin Lab: This would involve taking the present model and adapting it to Microcystis. The basic structure would be the same, except that Microcystis does not fix N. This is easily handled in the model by “knocking out” nifH and associated genes. Then the model would need to be calibrated to observations of Microcystis. Then, the toxin production genes and pathways would have to be programmed and calibrated/validated. This will require more work, comparable to the Anabaena Lab project, and a good PhD thesis topic.
Anabaena Energy Lab: The present model does not explicitly track intracellular energy (i.e. in terms of ATP or equivalent) and tie it to growth. For example, the cost of fixing one N2 vs. taking up and reducing one NO3 is not explicitly considered in the model. I could, for example, simply increase the NifH rate and then the cells would grow faster on N2 than NO3. This change would make the model more mechanistically detailed and correct. This will require more work, comparable to the Anabaena Lab project, again a good PhD topic.
Microcystis Field: Once the Microcystis model is coded we could apply it to a real lake. Again, this would require that the lake is dominated by Microcystis. Of course, it is unlikely that we would find such a system anywhere [this is a Taihu insider joke].
Anabaena/Microcystis Lab Competition: This came out of some discussion and ideas we had about light energy and competition between these species.
Anabaena/Microcystis Competition Field: Finally, the whole model can be used to explore the competition between these two species in the field.
Link to the paper:
Link to the YouTUBE movie: