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:
