White Paper Title: 
Reaction Progress and Microbial Communities

Reaction progress is a way to quantify the extent to which a system has changed from an initial state far from equilibrium to the corresponding equilibrium state. It is an explicit evaluation of the state of disequilibrium in a system. Chemotrophic microbes depend on disequilibria for energy, and only populate systems that have not yet reached equilibrium. The extent of progress of an energy- or nutrient-providing reaction is reflected by microbial gene expression, probably through tipping-point phenomena. Communities of chemotrophic microbes work together to dissipate part of the energy present in their habitats. It follows that, in addition to triggering gene expression, the structure of microbial communities may be dictated, at least in part, by the state of reaction progress in a natural system. If so, there should be ways to use quantified states of reaction progress to predict the microbial activity as well as the compositions of microbial communities, and vice versa.

Coordinating biological, petrological, hydrological and geochemical sampling allows data integration and tests of hypotheses about the interplay of reaction progress, gene expression and community structure. As an example, genomic and phylogenetic studies can reveal the structure and composition of microbial communities. Snapshot views of this type can be related to the abiotic parts of the same system by calculating multi-component reaction progress. Doing so is facilitated with inclusive, simultaneously collected compositional data from the natural system, and a thermodynamic model that incorporates minerals, aqueous solutions, organic compounds and microorganisms.

Current efforts to evaluate thermodynamic properties of microorganisms rely exclusively on thermodynamic properties of proteins (Dick and Shock, 2010). There is certainly more to organisms than their proteins. Nevertheless, close agreement is possible between microbial community structures obtained through environmental genomic data and those predicted by thermodynamic calculations. Perhaps the timing is right for a convergence of molecular biological data and geochemical data through the reference frame of reaction progress.

Dick, J.M. and Shock, E.L. (2010) Chemical equilibrium among microbial proteins in hot spring biofilms. PLoS Computational Biology (submitted).