Systems-informed genome mining for electroautotrophic microbial production

Abstract

Microbial electrosynthesis (MES) systems can store renewable energy and CO2 in many-carbon molecules inaccessible to abiotic electrochemistry. Here, we develop a multiphysics model to investigate the fundamental and practical limits of MES enabled by direct electron uptake and we identify organisms in which this biotechnological CO2-fixation strategy can be realized. Systematic model comparisons of microbial respiration and carbon fixation strategies revealed that, under aerobic conditions, the CO2 fixation rate is limited to <6 μmol/cm2/hr by O2 mass transport despite efficient electron utilization. In contrast, anaerobic nitrate respiration enables CO2 fixation rates >50 μmol/cm2/hr for microbes using the reductive tricarboxylic acid cycle. Phylogenetic analysis, validated by recapitulating experimental demonstrations of electroautotrophy, uncovered multiple probable electroautotrophic organisms and a significant number of genetically tractable strains that require heterologous expression of <5 proteins to gain electroautotrophic function. The model and analysis presented here will guide microbial engineering and reactor design for practical MES systems.

Genomically mined acoustic reporter genes for real-time in vivo monitoring of tumors and tumor-homing bacteria

“…We sought to make acoustic proteins widely useful in in vivo biological research and potential clinical applications by developing ARGs that, when expressed heterologously in either bacteria or mammalian cancer cell lines, could produce GVs with strong non-linear ultrasound contrast and enable long-term expression under physiological conditions. We used a genomic mining approach-previously applied to improving fluorescent proteins [11][12][13][14] , opsins [15][16][17] , Cas proteins [18][19][20][21][22] and other biotechnology tools [23][24][25][26][27][28] -to identify ARGs with improved properties, which we subsequently optimized through genetic engineering. By cloning and screening 15 distinct polycistronic operons chosen from a diverse set of 288 GV-expressing species representing a broad phylogeny, we identified two GV gene clusters-from Serratia sp.…”

Choice of Microbial System for In-Situ Resource Utilization on Mars

“…Light-independent, lithoautotrophy can fix carbon by relying on chemically provided reducing power. On Mars, this could either directly be electricity through microbial electrosynthesis in bio-electrochemical systems (Moscoviz et al, 2016;Abel et al, 2020;Chen et al, 2020a), or indirectly by means of hydrogen or (organoautotrophically) formate, both of which can also be generated electrochemically (Kracke et al, 2020;Abel and Clark, 2021). Use of other electron donors like, e.g., sulphide, sulphur and iron (II) is theoretically possible, but technically less feasible (crustal materials from Mars are in principle able to support lithotrophic growth (Milojevic et al, 2021), but mining and purifying these in quantities that could support biotechnological processes is likely not viable).…”

Efficiency Estimates for Electromicrobial Production of Branched-chain Hydrocarbons

“…Electromicrobial production (EMP) could enable highly efficient production of carbon-neutral drop-in biofuels. EMP is a broadly-encompassing term for a group of technologies that aim to combine electricity and microbial metabolism for conversion of simple molecules like CO2, CO, HCOO -, and N2 into complex, energy dense molecules like food and biofuels [7][8][9][10][11][12][13][14][15][16] . EMP includes technologies like microbes that assimilate electrochemically-reduced CO2 like formate 14,17 ; H2-oxidizing, CO2-fixing systems like the Bionic Leaf 18,19 ; microbe-semiconductor hybrids 20 ; and microbes that can directly absorb electricity through processes like extracellular electron uptake (EEU) 8,21,22 .…”