Enable production of energy-dense and carbon-neutral transportation fuels from lignocellulosic feedstocks and oil crops.

Design rhizosphere microbiomes that enable robust growth of feedstock crops (e.g., switchgrass, sorghum) on marginal lands (i.e., land with worse irrigation, fewer nutrients in soil).

• Technical Achievement: Engineer soil microbiomes to capture atmospheric carbon and increase soil organic carbon in marginal lands.
• Technical Achievement: Establish designer rhizospheres that selectively capture and concentrate chemicals to increase nutrient acquisition (e.g., nitrogen, phosphorous, iron and other trace metals).

Engineer microbiomes capable of producing fuel from lignocellulosic feedstocks and oil crops.

• Technical Achievement: Design microbiomes that can hand off metabolites between organisms, so biocatalysis is performed by individual organisms optimized for each step (i.e., bacteria are suboptimal for production of poly-ketide synthesis, but many biosynthetic gene clusters come from fungi so the natural host could be used).
• Technical Achievement: Engineer and optimize extremophiles so that they can produce higher titers of butanol from biomass.
• Technical Achievement: Engineer microbiomes that can withstand phase-separating concentrations of energy-dense fuels.
• Technical Achievement: Build microbiomes that produce and secrete lignocellulolytic cocktails that can process all components of lignocellulose, rather than individual enzymes.
• Technical Achievement: Develop communities that are resistant to inhibitors found in crude plant feedstocks to enable enzyme production in situ.

Engineer microbiomes to increase carbon utilization from feedstocks (e.g., sugars, carbon dioxide, organic acids).

• Technical Achievement: Engineer mixotrophy/simultaneous utilization of all available carbon sources, rather than catabolite repression, to decrease processing time.
• Technical Achievement: Engineer microbiomes to capture and recycle lost carbon of biomass generation for energy production, by catabolizing a given species once it is no longer needed.
• Technical Achievement: Engineer ecological succession, creating a microbiome that progresses through different feedstocks (e.g., carbon dioxide/lignocellulose to sugars, then fermentation acids from the first generation are used to produce compounds, then dead microbes from first generation are consumed) to capture all available carbon in a system.¹Brislawn, C. J., Graham, E. B., Dana, K., Ihardt, P., Fansler, S. J., Chrisler, W. B., Cliff, J. B., Stegen, J. C., Moran, J. J., & Bernstein, H. C. (2019). Forfeiting the priority effect: Turnover defines biofilm community succession. The ISME Journal, 13(7), 1865–1877. View Publication
• Technical Achievement: Engineer co-fermentation processes to increase gas (e.g., carbon dioxide, acetate) consumption rate and reduce microbiome toxicity arising from gas accumulation.

Engineer microbiome pretreatments to break down feedstocks, rather than chemical treatments or heating.

• Technical Achievement: Domesticate natural microbial communities that degrade lignocellulose (e.g., herbivore and insect gut microbiomes, wetlands/swamps).
• Technical Achievement: Using natural communities as a starting point, optimize microbiomes to degrade lignocellulose at increasing scales (e.g., pilot-scale, mid-sized, industrial).

Reduce environmental impacts of conventional energy generation processes.

Engineer microbiomes to reduce environmental impacts of mining (see also: Environmental Biotechnology).

• Technical achievement: Engineer microbiomes to extract valuable metals (e.g., rare earth elements) from electronic waste.²Kwok, R. (2019). Inner Workings: How bacteria could help recycle electronic waste. Proceedings of the National Academy of Sciences, 116(3), 711–713. View Publication
• Technical achievement: Engineer communities that can grow in mining waste and retain moisture, to reduce toxic dust from spreading in the environment.
• Technical achievement: Engineer communities that can sequester valuable metals from tailings and/or waste streams. Program taxis cascades to assist in recovery of these cells and the sequestered metals.
• Technical achievement: Program sentinel cells to detect pollutants in areas near mine to detect and mitigate problems at an early stage.

Engineer microbiome-enhanced oil production at the source.

• Technical achievement: Engineer microbial communities that can ‘clean’ dirty fossil fuels by removing contaminants or pollutants, or convert dirty fossil fuels to cleaner fuel sources (e.g., coal converted to natural gas).³Sharma, A., Jagarapu, A., Micale, C., Walia, D., Jackson, S., & Dhurjati, P. S. (2018). Modeling Framework for Biogenic Methane Formation from Coal. Energy & Fuels, 32(8), 8453–8461. View Publication
• Technical achievement: Develop communities that reduce souring (e.g., as a result of hydrogen sulfide gas) production in oilfields to lower corrosion and capital costs.
• Technical achievement: Develop communities that produce gases and/or surfactants in situ to mobilize trapped oil.
• Technical achievement: Develop communities to produce organic acids in situ to dissolve rock formations and mobilize oil without using chemical surfactants or fracking.

Footnotes

1. Brislawn, C. J., Graham, E. B., Dana, K., Ihardt, P., Fansler, S. J., Chrisler, W. B., Cliff, J. B., Stegen, J. C., Moran, J. J., & Bernstein, H. C. (2019). Forfeiting the priority effect: Turnover defines biofilm community succession. The ISME Journal, 13(7), 1865–1877. https://doi.org/10.1038/s41396-019-0396-x
2. Kwok, R. (2019). Inner Workings: How bacteria could help recycle electronic waste. Proceedings of the National Academy of Sciences, 116(3), 711–713. https://doi.org/10.1073/pnas.1820329116
3. Sharma, A., Jagarapu, A., Micale, C., Walia, D., Jackson, S., & Dhurjati, P. S. (2018). Modeling Framework for Biogenic Methane Formation from Coal. Energy & Fuels, 32(8), 8453–8461. https://doi.org/10.1021/acs.energyfuels.8b01298