Hays et al. 2015

Citation

Hays, S. G., Patrick, W. G., Ziesack, M., Oxman, N., & Silver, P. A. (2015). Better together: engineering and application of microbial symbioses. Current Opinion in Biotechnology, 36, 40-49.

Links

• https://scholar.google.com/scholar?cluster=386145057668943362
• https://www.sciencedirect.com/science/article/pii/S095816691500107X
• http://hawaiireedlab.com/pdf/h/haysetal2015.pdf (internal lab link only)

Published Abstract

Symbioses provide a way to surpass the limitations of individual microbes. Natural communities exemplify this in symbioses like lichens and biofilms that are robust to perturbations, an essential feature in fluctuating environments. Metabolic capabilities also expand in consortia enabling the division of labor across organisms as seen in photosynthetic and methanogenic communities. In engineered consortia, the external environment provides levers of control for microbes repurposed from nature or engineered to interact through synthetic biology. Consortia have successfully been applied to real-world problems including remediation and energy, however there are still fundamental questions to be answered. It is clear that continued study is necessary for the understanding and engineering of microbial systems that are more than the sum of their parts.

Published Highlights

• Microbial communities are naturally abundant.
• Natural symbioses exhibit increased robustness and metabolic capabilities.
• Technological advances in environmental control are applied to microbial cocultures.
• Synthetic biology can be used to engineer microbial communities.
• Microbial consortia are well suited for application to real-world problems.

Recommended Reading

• Bourdakos, N., Marsili, E., & Mahadevan, R. (2014). A defined co‐culture of Geobacter sulfurreducens and Escherichia coli in a membrane‐less microbial fuel cell. Biotechnology and Bioengineering, 111(4), 709-718.
• Cerqueda-García, D., Martínez-Castilla, L. P., Falcon, L. I., & Delaye, L. (2014). Metabolic analysis of Chlorobium chlorochromatii CaD3 reveals clues of the symbiosis in ‘Chlorochromatium aggregatum’. The ISME Journal, 8(5), 991.
• Connell, J. L., Ritschdorff, E. T., Whiteley, M., & Shear, J. B. (2013). 3D printing of microscopic bacterial communities. Proceedings of the National Academy of Sciences, 201309729.
• Drachuk, I., Suntivich, R., Calabrese, R., Harbaugh, S., Kelley-Loughnane, N., Kaplan, D. L., ... & Tsukruk, V. V. (2015). Printed dual cell arrays for multiplexed sensing. ACS Biomaterials Science & Engineering, 1(5), 287-294.
• Grube, M., Cernava, T., Soh, J., Fuchs, S., Aschenbrenner, I., Lassek, C., ... & Berg, G. (2015). Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics. The ISME Journal, 9(2), 412.
• Ho, A., De Roy, K., Thas, O., De Neve, J., Hoefman, S., Vandamme, P., ... & Boon, N. (2014). The more, the merrier: heterotroph richness stimulates methanotrophic activity. The ISME Journal, 8(9), 1945.
• Kotula, J. W., Kerns, S. J., Shaket, L. A., Siraj, L., Collins, J. J., Way, J. C., & Silver, P. A. (2014). Programmable bacteria detect and record an environmental signal in the mammalian gut. Proceedings of the National Academy of Sciences, 201321321.
• Mee, M. T., Collins, J. J., Church, G. M., & Wang, H. H. (2014). Syntrophic exchange in synthetic microbial communities. Proceedings of the National Academy of Sciences, 201405641.
• Minty, J. J., Singer, M. E., Scholz, S. A., Bae, C. H., Ahn, J. H., Foster, C. E., ... & Lin, X. N. (2013). Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proceedings of the National Academy of Sciences, 201218447.
• Song, H., Ding, M. Z., Jia, X. Q., Ma, Q., & Yuan, Y. J. (2014). Synthetic microbial consortia: from systematic analysis to construction and applications. Chemical Society Reviews, 43(20), 6954-6981.
• Weber, M. F., Poxleitner, G., Hebisch, E., Frey, E., & Opitz, M. (2014). Chemical warfare and survival strategies in bacterial range expansions. Journal of The Royal Society Interface, 11(96), 20140172.

Notes

This review focuses on the emergent properties of coculturing microbes together and how this can have advantages, both for the microbes and for biological engineering (Synthetic Biology) goals. The authors refer to this beneficial coculturing situation as consortia (referring to the term consortium in the business world of independent companies working together for a mutually beneficial outcome). Consortia is also used in the literature to describe Chlorochromatium aggregatum.

They refer to lichens and biofilms as examples of beneficial properties of increased robustness compared to axenic (consisting of only a single cell type) cultures.

Chlorochromatium aggregatum is used as an example of division of labor. One bacteria is photosynthetic epibiont and rides on a motile β-proteobacter towards light. In return the β-proteobacter, which has a reduced genome, gets much of its energy from the epibiont.

Most bacteria cannot be cultured in the lab using standard techniques. How much is the interdependence of bacteria playing a role in this? Different bacteria could be carrying out different necessary steps to metabolize resources and share the result (the authors mention this specifically in the "membrane separation" paragraph). (One form of this in microbes is known as syntrophy, "cross feeding".) It is easy to image an artificial scenario in the lab where two bacteria resistant to two different antibiotics can only be grown on media containing both antibiotics if they are co-cultured; each bacteria breaking down one of the antibiotics in its immediate surroundings. The authors point out an example in E. coli auxotrophs (Mee et al. 2014).

After introducing some naturally occurring examples the authors turn attention toward engineering consortia, "building a system in an effort to understand it". The tools used to do this include microfluidics, separation of microbes by membranes, and printing the microbes in one, two, and three dimensions (coaxial microbe containing fibers, tracks in agarose, inkjet printing, and 3D printing).

Different types of communication that enable emergent behaviors are discussed: quorum sensing and conjugation.

A model of the three way Rock-Paper-Scissors dynamic is mentioned as well as engineering a NOR logic gate.

Bioremediation is mentioned as one application of microbial consortia. Some pollutants and toxic environments may take many biochemical steps or require tolerance of many different compounds, which might be addressed by coculturing. Biofuel production is also mentioned with the example of coculturing E. coli and a fungus to convert cellulose to isobutanol. (When I mentioned this to Dr. de Couet he suggested flipping this around. Producing paper with microbes instead of trees.) One cool application combines both bioremediation and energy production with microbial fuel cells; electricity is generated directly by microbes treating wastewater (Logan 2009; Bourdakos et al. 2014).

Potential health applications are also mentioned such as ssensing and sending signals in the gut (Kotula et al. 2014).

Some of the students in ZOOL 490B Synthetic Biology felt that "rationally" (p. 43 in the first sentence under "Synthetic biology") implied that the goal of the engineering was good or useful rather than using logical steps to generate an expected outcome.

There appears to be a mistake in Figure 3a. Both types of bacteria are illustrated as A⁺ B^-. There also appears to be a mistake at the beginning of the references; there are two "* of special interest" lines. Reference 62 Opitz/Weber et al. (2014) seems to have the wrong author order.

Terms

• Axenic - A single species culture.
• Biofilm - Cells becoming embedded in an extracellular matrix, adhering to each other, and to a surface.
• Epibiont - An organism that lives on the surface of another.
• Exoelectrogen - An organism capable of extracellular electron transfer.
• Scotophobotaxis - "Fear-of-the-dark movement". Microorganisms avoiding movement out of light or returning to light from a darkened area.
• Syntrophic - "cross feeding". One organism living off the products of another.