University of Massachusetts Amherst

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ARO Grant of $650,000 Supports Research to Define the Roles of Bacteria in Biofilm Communities

Michael Henson

Michael Henson

Professor Michael Henson of the Chemical Engineering Department at the University of Massachusetts Amherst is one of the researchers for a three-year, $650,000 grant to support his research into the roles that various bacteria play in microbial communities. The research project is entitled “Development of Robust Microbial Communities through Engineered Biofilms.” The grant from the U.S. Army Research Office, or ARO, will support research into defining the functions of bacteria in various biofilm (or any group of microorganisms in which cells stick to each other) communities, thereby creating such beneficial applications as modeling new strategies for liquid biofuel production.

Henson is directing the UMass Amherst research on the large ARO project. As one good example of his research, Henson said, the same experimental and computer-modeling techniques his team will employ to design a three-species biofilm for converting agricultural plant waste into isobutanol – a second-generation liquid biofuel – can also be used to engineer other microbial systems.

Henson is working on the ARO project with Ross Carlson, a professor in Montana State University’s (MSU) Department of Chemical and Biological Engineering. According to an article published at MSU, most bacteria live within diverse communities attached to surfaces and tend to organize themselves strategically for optimal survival. As the article noted, each species in a particular community of bacteria has a different task to maintain the biofilm's effective functioning. These microscopic arrangements are similar to human communities comprised of people doing the various jobs required for the whole group to survive, thrive, and grow.

The same holds true for microbes, the MSU article pointed out. But little is yet known about how these communities are structured. Henson and Carlson hope to discover the roles that various bacteria play within a particular microbial biofilm and how they organize themselves within the biofilm to achieve maximum benefit for the whole community. With this knowledge, aided and abetted by the computer-modeling and experimentation the researchers will be conducting, they can enhance the function of good microbial communities and counter the activity of bad ones.

Henson’s ARO proposal explained that microbial biofilms are fundamentally important in environmental, medical, and engineered systems. In fact, a major goal of current biofuels research is to engineer synthetic microbial communities that mimic naturally occurring biofilms for lignocellulose conversion to renewable liquid fuels. While progress towards engineering synthetic communities has been made, existing approaches are largely based on well-mixed planktonic cultures which fundamentally lack the three-dimensional structure and therefore function of naturally occurring microbial biofilms.

The foundational design principles of biofilm groups are mostly unknown due largely to the complexity of these naturally occurring biofilm communities; for instance, as the proposal pointed out, a typical gram of agricultural soil contains more than 8,000 species, many growing as biofilms.

“We believe that carefully engineered, tunable biofilm consortia hold transformational potential for diverse applications of interest to the ARO,” the proposal said. “Our research will establish a blueprint for modeling, designing, and engineering biofilm communities using a combination of in silico genome-enabled approaches and biofilm experimental methods. We will show that these engineered biofilms can be spatially structured to maximize beneficial properties based on metabolite cross-feeding, minimization of deleterious species interactions, and enhanced synthesis of targeted metabolites.”

As a proof-of-concept, the researchers selected isobutanol as a model product due to its potential as a drop-in transportation fuel with a higher energy density than ethanol fuel. The research will produce a tractable, synthetic cellulose-degrading and isobutanol-synthesizing biofilm consortium comprised of three species representing distinct functional roles: an anaerobic cellulosic degrader Clostridium phytofermentans; a facultative sugar utilizer Escherichia coli engineered for isobutanol synthesis; and an anaerobic organic acid oxidizer/iron(III) reducer Geobacter sulfurreducens.

The first aim of the research is to develop and test a metabolic modeling framework for cellulose-to-biofuel multispecies consortia biofilms in a dynamic, spatially resolved format. Genome-scale metabolic models will be constructed for the three bacterial species above. The second aim is to develop and implement spatially resolved analytical methods for measuring cellulose-degrading biofilm mass and energy fluxes to quantify physiological similarities and differences between consortia and monoculture biofilms to inform model development. The third aim is to predict and test spatially resolved metabolic responses to culturing perturbations, including electron donor/acceptor perturbations and introduction of competing bacterial species with iterative loops of model and hypothesis refinement.

As Henson explained, “The immediate goal of this research is to demonstrate that the spatial organization of bacteria within multispecies biofilms can be controlled by imposing gradients of electron donors and acceptors that the bacteria need to grow. As a proof-of-concept, we will demonstrate the approach both experimentally and computationally for a three-species engineering system for conversion of the plant material cellulose to the second generation biofuel isobutanol. The longer term goal of the work is to develop a general methodology for manipulating biofilm spatial organization that will enhance the function of engineered biofilms and allow more effective eradication of deleterious biofilms involve in human infections.”

Henson and Carlson were co-authors of a paper on human infections, entitled “Metabolic Modeling of a Chronic Wound Biofilm Consortium Predicts Spatial Partitioning of Bacterial Species,” which was published on September 7, 2016, in BMC Systems Biology, an open-access journal that publishes original research on biological systems.

The computational models and experimental methods will be iteratively refined, yielding a blueprint of consortium acclimations and interactions that lead to the emergent biofilm properties of increased nutrient utilization and enhanced stress tolerance. This knowledge will permit rational development of design strategies based on enhancing the emergent properties associated with consortia interactions. The researchers will test such strategies to enable biofilm conversion of cellulose to isobutanol.

As the researchers concluded, “This project represents an effort to bring the collective talents of the interdisciplinary research team to bear on a synthetic microbial biofilm consortium capable of converting waste cellulosic material into useful bioproducts such as isobutanol.” (February 2017)