Carbon dioxide, a gas that our lungs exhale and is composed of one carbon atom bonded to two oxygen atoms, can harm the central nervous system if inhaled in high concentrations. Some strains of Escherichia coli (E. coli) bacteria found in raw meat, unpasteurized dairy products, and juices and water can cause serious, even fatal infections.
But scientists at the Weizmann Institute of Science in Rehovot have created in their labs a strain of E. coli that grows by consuming carbon dioxide instead of sugars or other inorganic molecules. Such bacteria could eventually contribute to new, carbon-efficient technologies that reduce man’s dependence on carbon fuels such as petroleum and even produce food.
“The living world is largely divided into autotrophs that convert CO2 into biomass and heterotrophs that consume organic compounds,” the authors wrote. “In spite of the widespread interest in renewable energy storage and more sustainable food production, the engineering of industrially relevant heterotrophic model organisms to use CO2 as their sole carbon source has so far remained an outstanding challenge.”
The Israelis’ achievement is a milestone, say, scientists, because it drastically alters the inner workings of one of biology’s most popular model organisms. And in the future, CO2-eating E. coli could be used to make organic carbon molecules that could be used as biofuels or to produce food. Products made in this way would have lower emissions compared with conventional production methods and could potentially remove the gas from the air. The work has just been published in the journal Cell.
Ewen Callaway wrote in the journal Nature: “It’s like metabolic heart transplantation,” commented Tobias Erb, a biochemist and synthetic biologist at the Max Planck Institute for Terrestrial Microbiology in Marburg, Germany who wasn’t involved in the study. “This is a proof-of-concept paper,” agreed Erb. “It will take a couple of years until we see this organism applied.”
Plants and photosynthetic cyanobacteria – aquatic microbes that produce oxygen – use the energy from light to transform – or fix – CO2 into the carbon-containing building blocks of life, including DNA, proteins and fats. But these organisms can be hard to genetically modify, which has slowed efforts to turn them into biological factories.
By contrast, E. coli is relatively easy to engineer, and its fast growth means that changes can be quickly tested and tweaked to optimize genetic alterations. But the bacterium prefers to grow on sugars such as glucose — and instead of consuming CO2, it emits the gas as waste.
Prof. Ron Milo, a systems biologist at the Rehovot institute and his team have spent the past 10 years overhauling E. coli’s diet. In 2016, they created a strain that consumed CO2, but the compound accounted for only a fraction of the organism’s carbon intake; the rest was an organic compound that the bacteria were fed, called pyruvate.
The bacteria have not just sworn off sugar – they have stopped eating all of their normal solid food, existing instead of carbon dioxide from their environment and building all of their biomass from air.
In their latest work, Milo and his team used a mix of genetic engineering and lab evolution to create a strain of E. coli that can get all its carbon from CO2. First, they gave the bacterium genes that encode a pair of enzymes that allow photosynthetic organisms to convert CO2 into organic carbon. Plants and cyanobacteria power this conversion with light, but that wasn’t feasible for E. coli. Instead, Milo’s team inserted a gene that lets the bacterium glean energy from an organic molecule called formate.
Even with these additions, the bacterium refused to swap its sugar meals for CO2. To further tweak the strain, the researchers cultured successive generations of the modified E. coli for a year, giving them only minute quantities of sugar, and CO2 at concentrations about 250 times those in Earth’s atmosphere. They hoped that the bacteria would evolve mutations to adapt to this new diet. After about 200 days, the first cells capable of using CO2 as their only carbon source emerged. And after 300 days, these bacteria grew faster in the lab conditions than did those that could not consume CO2.
The CO2-eating (autotrophic) E. coli strains can still grow on sugar — and would use that source of fuel over CO2, given the choice, noted Milo. Compared with normal E. coli, which can double in number every 20 minutes, the autotrophic E. coli are lazy dividing every 18 hours when grown in an atmosphere that is 10% CO2. They are not able to subsist without sugar on atmospheric levels of CO2 – currently 0.041%.
Milo and his team hope to make their bacteria grow faster and live on lower levels of CO2. They are also trying to understand how E. coli evolved to eat CO2: changes in just 11 genes seemed to allow the switch, and they are now working on determining how.
The work is a “milestone” and shows the power of melding engineering and evolution to improve natural processes, said Cheryl Kerfeld, a bioengineer at Michigan State University in East Lansing and the Lawrence Berkeley National Laboratory in California.
Already, E. coli is used to make synthetic versions of useful chemicals such as insulin and human growth hormone. Milo says that his team’s work could expand the products the bacteria can make, to include renewable fuels, food, and other substances. But he doesn’t see this happening soon.
Just giving the bacteria the “means of production” was not enough, it turned out, for them to make the switch. There was still a need for another trick to get the bacteria to use this machinery properly, and this involved a delicate balancing act. Together with Roee Ben-Nissan, Yinon Bar-On and other members of Milo’s team in the Institute’s plant and environmental sciences department, Gleizer used lab evolution, as the technique is known; in essence, the bacteria were gradually weaned off the sugar they were used to eating.
At each stage, cultured bacteria were given just enough sugar to keep them from complete starvation, as well as plenty of CO2 and formate. As some “learned” to develop a taste for CO2 (giving them an evolutionary edge over those that stuck to sugar), their descendants were given less and less sugar until after about a year of adapting to the new diet some of them eventually made the complete switch, living and multiplying in an environment that served up pure CO2.
To check whether the bacteria were not somehow “snacking” on other nutrients, some of the evolved E. coli were fed CO2 containing a heavy isotope – C13. Then the bacterial body parts were weighed, and the weight they had gained checked against the mass that would be added from eating the heavier version of carbon. The analysis showed the carbon atoms in the body of the bacteria were all extracted directly from CO2 alone.
The research team then set out to characterize the newly-evolved bacteria. What changes were essential to adapting to this new diet? While some of the genetic changes they identified may have been tied to surviving hunger, others appeared to regulate the synchronization of the steps of making building blocks through accumulation from CO2. “The cell needs to balance between toxic congestion and bankruptcy,” said Bar-On. Yet other changes the team noted had to do with transcription – regulating how existing genes are turned on and off. “Further research will hopefully uncover exactly how these genes have adjusted their activities,” added Ben-Nissan.
The researchers believe that the bacteria’s new “health kick” could ultimately give Earth a healthier environment. Milo points out that today, biotech companies use cell cultures to produce commodity chemicals. Such cells – yeast or bacteria – could be induced to live on a diet of CO2 and renewable electricity and thus be weaned from the large amounts of corn syrup they live on today.
Bacteria could be further adapted so that rather than taking their energy from formate, they might be able to get it straight up – such as electrons from a solar collector – and then store that energy for later use as fuel in the form of carbon fixed in their cells. Such fuel would be carbon-neutral if the source of its carbon was atmospheric CO2.
“Our lab was the first to pursue the idea of changing the diet of a normal heterotroph (one that eats organic substances) to convert it to autotrophism,” concluded Milo. “It sounded impossible at first, but it has taught us numerous lessons along the way, and in the end, we showed it indeed can be done. Our findings are a significant milestone toward our goal of efficient, green scientific applications.”
