NSF Microbial Connectivity Project
Investigating the connectivity of microbial food webs using
thermodynamic models, stable isotope probing and genomics
NSF DEB project (award #1655552)
Additional support from Simons Foundation (award #549941, JJV) CBIOMES
Prinicple Investigators:
Joe Vallino (MBL)
Julie Huber (WHOI)
Postdoctoral Investigator:
Olivia Ahern
Previous Postdoctoral Investigators:
Ashley Bulseco
Amy Smith
Abstract
The habitability of Earth is maintained in part by the actions of
microscopic organisms that continuously breakdown dead organic material
and recycle the chemical elements needed by all living organisms. The
Earth's microbiome, as it is also known as, consists of bacteria and
archaea as well as protists and viruses that prey upon them. The
complex and dynamic milieu of interacting microscopic organisms can be
difficult to disentangle and understand because as many as a billion
bacteria and archaea, and 10 billion viruses, can be found in a liter
of water or a gram of soil. Recent advances in molecular biology are
beginning to allow scientists to determine which microscopic organisms
are present in an environmental sample, as well as how population
numbers change over time and what the organisms are doing, such as
consuming carbon dioxide from the atmosphere. To understand and predict
how microbial communities respond to environmental changes, or how they
can be used in biotechnology, energy production or remediation of
pollution, scientists construct mathematical models. Properly
representing all the microbial interactions in extremely diverse
microscopic worlds in a mathematical model is a great challenge.
Researchers for this project have developed a novel modeling approach,
which exploits a theory that argues complex systems - ones that can be
assembled in many different ways - will likely arrange and organize
themselves to maximize their consumption of usable energy, such as
found in food or sunlight. The theory, known as maximum entropy
production (MEP), also predicts how microscopic communities should be
structured; that is, who eats whom. To test the theory, researchers
will use laboratory microcosms combined with molecular biological
techniques to determine the structure of natural microbial communities
and compare them to predictions made by the model. The project also
will support one postdoctoral researcher, and provide research training
for 2 to 5 undergraduate students each year.
Preliminary modeling results based on the MEP theory show that
microbial food webs constructed of strong predator-prey chains are
effective at utilizing resources and dissipating free energy, while
highly connected generalist food webs prevent effective use of
resources and do not locate MEP solutions. The hypothesis that
microbial communities organize to form strongly coupled predator-prey
chains that are weakly interconnected will be tested with laboratory
chemostats inoculated with natural microbial communities. Food web
structure will be assessed with stable isotope probing techniques and
the active consumers and their predators identified by sequencing of
the labeled community. The results from the experiments will not only
facilitate development of Darwin-based MEP models, but will also
contribute significantly to our theoretical understanding of how
microbial communities organize to facilitate the dissipation of
available free energy as well as to advance consumer-resource theory
for microbial systems that are the foundation of all ecosystems.
Proposal is here.