Significance: The microbial production of ethanol (bioethanol) is a massive commercialized technology. Though alcohols with longer carbon chains are chemically much better suited for current transportation needs, their biotechnological production remains challenging. Here we have engineered the model hyperthermophile Pyrococcus furiosus to produce various alcohols from their corresponding organic acids by constructing a synthetic route termed the AOR/AdhA pathway. Our study is also the first example, to our knowledge, of significant alcohol formation in an archaeon, emphasizing the biotechnological potential of novel microorganisms. Moreover, we show that carbon monoxide and hydrogen (syngas) can be used as the driving forces for alcohol production. The application of the AOR/AdhA pathway in syngas-fermenting microorganisms is potentially a game-changing platform technology for the production of longer bioalcohols.

The three major components of plant biomass, cellulose, hemicellulose and lignin, are highly recalcitrant and deconstruction involves thermal and chemical pretreatment. Microbial conversion is a possible solution, but few anaerobic microbes utilize both cellulose and hemicellulose and none are known to solubilize lignin. Herein, we show that the majority (85%) of insoluble switchgrass biomass that had not been previously chemically treated was degraded at 78 °C by the anaerobic bacterium Caldicellulosiruptor bescii. Remarkably, the glucose/xylose/lignin ratio and physical and spectroscopic properties of the remaining insoluble switchgrass were not significantly different than those of the untreated plant material. C. bescii is therefore able to solubilize lignin as well as the carbohydrates and, accordingly, lignin-derived aromatics were detected in the culture supernatants. From mass balance analyses, the carbohydrate in the solubilized switchgrass quantitatively accounted for the growth of C. bescii and its fermentation products, indicating that the lignin was not assimilated by the microorganism. Immunoanalyses of biomass and transcriptional analyses of C. bescii showed that the microorganism when grown on switchgrass produces enzymes directed at key plant cell wall moieties such as pectin, xyloglucans and rhamnogalacturonans, and that these and as yet uncharacterized enzymes enable the degradation of cellulose, hemicellulose and lignin at comparable rates. This unexpected finding of simultaneous lignin and carbohydrate solubilization bodes well for industrial conversion by extremely thermophilic microbes of biomass that requires limited or, more importantly, no chemical pretreatment.

Thermoanaerobacter kivui is one of the very few thermophilic acetogenic microorganisms. It grows optimally at 66°C on sugars but also lithotrophically with H ₂ + CO ₂ or with CO, producing acetate as the major product. While a genome-derived model of acetogenesis has been developed, only a few physiological or biochemical experiments regarding the function of important enzymes in carbon and energy metabolism have been carried out. To address this issue, we developed a method for targeted markerless gene deletions and for integration of genes into the genome of T. kivui . The strain naturally took up plasmid DNA in the exponential growth phase, with a transformation frequency of up to 3.9 × 10 ⁻⁶ . A nonreplicating plasmid and selection with 5-fluoroorotate was used to delete the gene encoding the orotate phosphoribosyltransferase ( pyrE ), resulting in a Δ pyrE uracil-auxotrophic strain, TKV002. Reintroduction of pyrE on a plasmid or insertion of pyrE into different loci within the genome restored growth without uracil. We subsequently studied fructose metabolism in T. kivui . The gene fruK (TKV_c23150) encoding 1-phosphofructosekinase (1-PFK) was deleted, using pyrE as a selective marker via two single homologous recombination events. The resulting Δ fruK strain, TKV003, did not grow on fructose; however, growth on glucose (or on mannose) was unaffected. The combination of pyrE as a selective marker and the natural competence of the strain for DNA uptake will be the basis for future studies on CO ₂ reduction and energy conservation and their regulation in this thermophilic acetogenic bacterium. IMPORTANCE Acetogenic bacteria are currently the focus of research toward biotechnological applications due to their potential for de novo synthesis of carbon compounds such as acetate, butyrate, or ethanol from H ₂ + CO ₂ or from synthesis gas. Based on available genome sequences and on biochemical experiments, acetogens differ in their energy metabolism. Thus, there is an urgent need to understand the carbon and electron flows through the Wood–Ljungdahl pathway and their links to energy conservation, which requires genetic manipulations such as deletion or overexpression of genes encoding putative key enzymes. Unfortunately, genetic systems have been reported for only a few acetogenic bacteria. Here, we demonstrate proof of concept for the genetic modification of the thermophilic acetogenic species Thermoanaerobacter kivui . The genetic system will be used to study genes involved in biosynthesis and energy metabolism, and may further be applied to metabolically engineer T. kivui to produce fuels and chemicals.

Microorganisms growing near the boiling point have enormous biotechnological potential but only recently have molecular engineering tools become available for them. We have engineered the hyperthermophilic archaeon Pyrococcus furiosus , which grows optimally at 100°C, to switch its end products of fermentation in a temperature-controlled fashion without the need for chemical inducers. The recombinant strain (LAC) expresses a gene ( ldh ) encoding lactate dehydrogenase from the moderately thermophilic Caldicellulosiruptor bescii (optimal growth temperature [ T _opt ] of 78°C) controlled by a “cold shock” promoter that is upregulated when cells are transferred from 98°C to 72°C. At 98°C, the LAC strain fermented sugar to produce acetate and hydrogen as end products, and lactate was not detected. When the LAC strain was grown at 72°C, up to 3 mM lactate was produced instead. Expression of a gene from a moderately thermophilic bacterium in a hyperthermophilic archaeon at temperatures at which the hyperthermophile has low metabolic activity provides a new perspective to engineering microorganisms for bioproduct and biofuel formation. IMPORTANCE Extremely thermostable enzymes from microorganisms that grow near or above the boiling point of water are already used in biotechnology. However, the use of hyperthermophilic microorganisms themselves for biotechnological applications has been limited by the lack of their genetic accessibility. Recently, a genetic system for Pyrococcus furiosus , which grows optimally near 100°C, was developed in our laboratory. In this study, we present the first heterologous protein expression system for a microorganism that grows optimally at 100°C, a first step towards the potential expression of genes involved in biomass degradation or biofuel production in hyperthermophiles. Moreover, we developed the first system for specific gene induction in P. furiosus . As the cold shock promoter for protein expression used in this study is activated at suboptimal growth temperatures of P. furiosus , it is a powerful genetic tool for protein expression with minimal interference of the host’s metabolism and without the need for chemical inducers.