Bottleneck/Challenge: Maintaining microbiome stability and ensuring that energy is not redirected towards biomass production.

Potential Solution: Engineer multiple functionally redundant pathways to prevent biomass generation and ensure continued biochemical production.

Bottleneck/Challenge: Only certain wavelengths of light are captured by any individual organism, so overall energy capture is low.

Potential Solution: Engineer communities that capture multiple wavelengths (i.e., a single wavelength band per organism) to maximize efficiency.

Bottleneck/Challenge: Lithoautotrophy does not use energy dense energy sources, and a lot of energy is used for biomass growth.

Potential Solution: Engineer genetic circuits that allow for biomass accumulation initially, but then switch to compound production at the expense of growth.

Bottleneck/Challenge: The 3-Hydroxypropionate bicycle accepts the most diverse selections of carbon substrates but is the most energy expensive, resulting in lower yields.

Potential Solution: Use directed evolution to drive model microbiomes towards more energy-efficient enzymes within the 3-Hydroxypropionate bicycle.

Bottleneck/Challenge: Carbon dioxide or bicarbonate concentration/compression can be achieved today through engineering solutions, but are energy intensive processes.

Potential Solution: Develop mechanisms to biologically concentrate carbon dioxide for efficient use.

Bottleneck/Challenge: Atmospheric carbon dioxide is present in low concentrations.

Potential Solution: Develop mechanisms to biologically concentrate carbon dioxide for efficient use.

Bottleneck/Challenge: Most known extracellular electron transfer processes only function under anaerobic conditions.

Potential Solution: Design microbiomes containing facultative anaerobes that can rapidly reduce/deoxygenate the growth environment to facilitate electrical energy production and extraction.

Bottleneck/Challenge: Acquiring dynamic and species-specific data for electrochemical reactions in a microbiome is difficult.

Potential Solution: Design methods to perform highly time-resolved mass spectrometry and capture reaction dynamics in a complex environment.

Bottleneck/Challenge: Energy can be lost, or slow to ramp up and down, when using naturally-occurring electron shuttles.

Potential Solution: Engineer nanowires on microbial surfaces to directly shuttle electrons within a microbiome or to an electrode. This could allow for electron transfer between reactors and may facilitate biosynthesis of NADH or another energy-storing compound.

Bottleneck/Challenge: Spatial organization of microbial species to maximize energy capture (e.g., light-exposed volume for photosynthesis) and extraction (e.g., contact surface area on electrodes).

Potential Solution: Engineer interspecies nanowires to facilitate electron or energy transfer between organisms that are not exposed to an electrode or energy source.

Bottleneck/Challenge: Evolutionary pressures will select for mutants/contaminating species that can use the ‘excess’ energy for biomass generation rather than biotransformation.

Potential Solution: Engineer voltage-dependent kill switches, so cells that use excess energy for biomass are selectively removed from the microbiome.