Engineered bacteria that feed on CO2 could lead to the development of carbon-neutral fuels

Such bacteria may, in the future, contribute to new, carbon-efficient technologies

Bacteria in the lab of Prof. Ron Milo of the Weizmann Institute of Science have not just sworn off sugar – they have stopped eating all of their normal solid food, existing instead on carbon dioxide (CO2) from their environment. That is, they were able to build all of their biomass from air. This feat, which involved nearly a decade of rational design, genetic engineering and a sped-up version of evolution in the lab, was reported this week in Cell. The findings point to means of developing, in the future, carbon-neutral fuels.

The study began by identifying crucial genes for the process of carbon fixation – the way plants take carbon from CO2 for the purpose of turning it into such biological molecules as protein, DNA, etc. The research team added and rewired the needed genes. They found that many of the “parts” for the machinery that were already present in the bacterial genome could be used as is. They also inserted a gene that allowed the bacteria to get energy from a readily available substance called formate that can be produced directly from electricity and air and which is apt to “give up” electrons to the bacteria.

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.

The bacteria’s new “health kick” could ultimately be healthy for the planet

To check whether the bacteria were not somehow “snacking” on other nutrients, some of the evolved E. coli were fed COcontaining 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,” says 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,” says Ben-Nissan.

The researchers believe that the bacteria’s new “health kick” could ultimately be healthy for the planet. 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 a substance such as formate, they might be able to get it straight up — say 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 (‘living on air’),” says 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.”

Learn more: The Greenest Diet: Bacteria Switch to Eating Carbon Dioxide



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Copper beds in hospitals have 95 percent fewer bacteria than conventional hospital beds

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A new study has found that copper hospital beds in the Intensive Care Unit (ICU) harbored an average of 95 percent fewer bacteria than conventional hospital beds, and maintained these low-risk levels throughout patients’ stay in hospital.

The research is published this week in Applied and Environmental Microbiology, a journal of the American Society for Microbiology.

“Hospital-acquired infections sicken approximately 2 million Americans annually, and kill nearly 100,000, numbers roughly equivalent to the number of deaths if a wide-bodied jet crashed every day,” said coauthor Michael G. Schmidt, PhD, Professor of Microbiology and Immunology, Medical University of South Carolina, Charleston. They are the eighth leading cause of death in the US.

Hospital beds are among the most contaminated surfaces in patient care settings. “Despite the best efforts by environmental services workers, they are neither cleaned often enough, nor well enough,” said Dr. Schmidt. Nonetheless, until recently, patient beds incorporating copper surfaces—long known to repel and kill bacteria—have not been commercially available.

Knowledge of copper’s antimicrobial properties dates back to ancient Ayurveda, when drinking water was often stored in copper vessels to prevent illness. In the modern medical era, numerous studies have noted copper’s antimicrobial properties.

However, until recently, no-one had designed acute–care hospital beds that enabled all high risk surfaces to be encapsulated in copper. “Based on the positive results of previous trials, we worked to get a fully encapsulated copper bed produced,” said Dr. Schmidt. “We needed to convince manufacturers that the risk to undertake this effort was worthwhile.”

This in situ study compared the relative contamination of intensive care unit (ICU) beds outfitted with copper rails, footboards, and bed controls to traditional hospital beds with plastic surfaces. Nearly 90 percent of the bacterial samples taken from the tops of the plastic rails had concentrations of bacteria that exceed levels considered safe.

“The findings indicate that antimicrobial copper beds can assist infection control practitioners in their quest to keep healthcare surfaces hygienic between regular cleanings, thereby reducing the potential risk of transmitting bacteria associated with healthcare associated infections,” said Dr. Schmidt.

With the advent of copper encapsulated hospital beds, dividends will likely be paid in improved patient outcomes, lives saved, and healthcare dollars saved.

Learn more: Copper Hospital Beds Kill Bacteria, Save Lives


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Bacteria that eat and breathe electricity have big potential

Pools of hot water like this are the home to bacteria that can eat and breathe electricity.

Last August, Abdelrhman Mohamed found himself hiking deep into the wilderness of Yellowstone National Park.

Unlike thousands of tourists who trek to admire the park’s iconic geysers and hot springs every year, the WSU graduate student was traveling with a team of scientists to hunt for life within them.

After a strenuous seven mile walk through scenic, isolated paths in the Heart Lake Geyser Basin area, the team found four pristine pools of hot water. They carefully left a few electrodes inserted into the edge of the water, hoping to coax little-known creatures out of hiding — bacteria that can eat and breathe electricity.

After 32 days, the team returned to the hot springs to collect the submerged electrodes. Working under the supervision of Haluk Beyenal, Paul Hohenschuh Distinguished Professor in the Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Mohamed and postdoctoral researcher Phuc Ha analyzed the electrodes.

Voila! They had succeeded in capturing their prey – heat-loving bacteria that “breathe” electricity through the solid carbon surface of the electrodes.

The WSU team, in collaboration with colleagues from Montana State University, published their research detailing the multiple bacterial communities they found in the Journal of Power Sources.

“This was the first time such bacteria were collected in situ in an extreme environment like an alkaline hot spring,” said Mohamed, adding that temperatures in the springs ranged from about 110 to nearly 200 degrees Fahrenheit.

These tiny creatures are not merely of academic interest.

They may hold a key to solving some of the biggest challenges facing humanity – environmental pollution and sustainable energy. Such bacteria can “eat” pollution by converting toxic pollutants into less harmful substances and generating electricity in the process.

“As these bacteria pass their electrons into metals or other solid surfaces, they can produce a stream of electricity that can be used for low-power applications,” said Beyenal.

Most living organisms – including humans – use electrons, which are tiny negatively-charged particles, in a complex chain of chemical reactions to power their bodies. Every organism needs a source of electrons and a place to dump the electrons to live. While we humans get our electrons from sugars in the food we eat and pass them into the oxygen we breathe through our lungs, several types of bacteria dump their electrons to outside metals or minerals, using protruding hair-like wires.

To collect bacteria in such an extreme environment over 32 days, Mohamed invented a cheap portable potentiostat, an electronic device that could control the electrodes submerged in the hot springs for long periods of time.

“The natural conditions found in geothermal features such as hot springs are difficult to replicate in laboratory settings,” said Beyenal. “So, we developed a new strategy to enrich heat-loving bacteria in their natural environment.”

Learn more: Capturing bacteria that eat and breathe electricity



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Capturing carbon dioxide and converting it into chemicals using bacteria in “spacesuits”

A 2D MOF wraps around the bacteria to form a soft cloak that expands as the bacteria grow and split. The MOF protects them from oxygen, the reverse of a spacesuit, which protects astronauts from the airlessness of space.

Just as spacesuits help astronauts survive in inhospitable environments, newly developed “spacesuits” for bacteria allow them to survive in environments that would otherwise kill them.

University of California, Berkeley, chemists developed the protective suits to extend the bacteria’s lifespan in a unique system that pairs live bacteria with light-absorbing semiconductors in order to capture carbon dioxide and convert it into chemicals that can be used by industry or, someday, in space colonies.

The system mimics photosynthesis in plants. But while plants capture carbon dioxide and, with the energy from sunlight, convert it to carbohydrates that we often eat, the hybrid system captures CO2 and light to make a variety of carbon compounds, depending on the type of bacteria.

The bacteria used in the experiment are anaerobic, which means they are adapted to live in environments without oxygen. The suit – a patchwork of mesh-like pieces called a metal-organic framework, or MOF – is impermeable to oxygen and reactive oxygen molecules, like peroxide, which shorten their lifespan.

The hybrid system could be a win-win for industry and the environment: It can capture carbon dioxide emitted by power plants and turn it into useful products. It also provides a biological way to produce needed chemicals in artificial environments such as spaceships and habitats on other planets.

“We are using our biohybrid to fix CO2 to make fuels, pharmaceuticals and chemicals, and also nitrogen fixation to make fertilizer,” said Peidong Yang, the S. K. and Angela Chan Distinguished Chair in Energy in UC Berkeley’s Department of Chemistry. “If Matt Damon wants to grow potatoes on Mars, he needs fertilizer.”

Yang, a faculty scientist at Lawrence Berkeley National Laboratory and a co-director of the Kavli Energy Nanoscience Institute, was referring to the actor who played the protagonist in the movie The Martian. Damon’s character was marooned on Mars and had to use his own waste as fertilizer to grow potatoes for food.

The research, funded by NASA through UC Berkeley’s Center for the Utilization of Biological Engineering in Space, will be posted online this week in advance of publication in the journal Proceedings of the National Academy of Sciences.

A hybrid of bacteria and semiconductor

Yang and his colleagues developed the hybrid bacterial system over the past five years based on their work on light-absorbing semiconductors such as nanowires: solid wires of silicon a few hundred nanometers across, where a nanometer is a billionth of a meter. Arrays of nanowires can be used to capture light and generate electricity, promising cheap solar cells.

When fed cadmium, the bacterium Moorella thermoacetica decorates itself with cadmium sulfide particles that absorb light, creating a hybrid artificial photosynthesis system that converts sunlight and carbon dioxide into valuable chemical products.

The hybrid system takes advantage of efficient light capture by semiconductors to feed electrons to anaerobic bacteria, which normally scavenge electrons from their environment to live. The goal is to boost carbon capture by the bacteria to churn out useful carbon compounds.

“We are interfacing these bugs with a semiconductor that overwhelms them with electrons, so they can do more chemistry,” Yang said. “But at the same time this process also generates all these reactive oxygen species, which are detrimental to the bugs. We are putting these bacteria in a shell so that if any of these oxidative species comes in, this first defense, the shell, decomposes them.”

The suit is made of a MOF mesh that wraps around the bacteria, covering it in patches. Wearing these MOF suits, the bacteria live five times longer at normal oxygen concentrations – 21 percent by volume – than without the suits, and often longer than in their natural environment, Yang said. Their normal lifespan ranges from weeks to months, after which they can be flushed from the system and replaced with a fresh batch.

In this experiment, the researchers used bacteria called Morella thermoacetica, which produce acetate (acetic acid, or vinegar), a common precursor in the chemical industry. Another one of their test bacteria, Sporomusa ovata, also produces acetate.

“We picked these anaerobic bacteria because their selectivity toward one chemical product is always 100 percent,” he said. “In our case, we picked a bug that gives us acetate. But you could select another bug to give you methane or alcohol.”

In fact, the bacteria that ferment the alcohol in beer and wine and turn milk into cheese and yoghurt are all anaerobic.

While Yang’s first experiments with the hybrid system paired bacteria with a bristle of silicon nanowires, in 2016 he discovered that feeding the bacteria cadmium encouraged them to decorate themselves with a natural semiconductor, cadmium sulfide, that acts as an efficient light absorber feeding the bacteria electrons.

In the current experiment, the researchers took bacteria decorated with cadmium sulfide and enshrouded them with a flexible, one nanometer thick layer of MOF. While a rigid MOF interfered with the bacteria’s normal process of growth and splitting, a zirconium-based MOF patch turned out to be soft enough to allow the bacteria to swell and divide while still clothed with MOF, after which new MOF in the solution re-clothed them.

“You can think of the 2D MOF like a sheet of graphene: a one-layer-thick cloak that covers the bacteria,” said co-author Omar Yaghi, a pioneer of MOFs and the James and Neeltje Tretter Chair in the Department of Chemistry. “The 2D MOF is floating in solution with the bacteria, and as the bacteria replicate they are covered further with the 2D MOF layer, so it protects the bacteria from oxygen.”

Yang and his colleagues are also working to improve the hybrid system’s efficiency of light capture, electron transfer and production of specific compounds. They envision combining these optimized capabilities with new metabolic pathways in these bacteria to produce ever more complex molecules.

“Once you fix or activate CO2 – and that is the most difficult part – you can use many existing chemical and biological approaches to upgrade them to fuels, pharmaceuticals and commodity chemicals,” he said.

Learn more: ‘Spacesuits’ protect microbes destined to live in space



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Artificial cells that can kill bacteria have been created

Biomedical engineers at UC Davis have created that mimic some of the properties of living cells. The artificial cells do not grow and divide, but could detect, react to and destroy bacteria in a lab dish. (Cheemeng Tan, UC Davis)

Lego block” artificial cells that can kill bacteria have been created by researchers at the University of California, Davis, Department of Biomedical Engineering. The work is reported Aug. 29 in the journal ACS Applied Materials & Interfaces.

“We engineered artificial cells from the bottom-up — like Lego blocks — to destroy bacteria,” said Assistant Professor Cheemeng Tan, who led the work. The cells are built from liposomes, or bubbles with a cell-like lipid membrane, and purified cellular components including proteins, DNA and metabolites.

“We demonstrated that artificial cells can sense, react and interact with bacteria, as well as function as systems that both detect and kill bacteria with little dependence on their environment,” Tan said.

The team’s artificial cells mimic the essential features of live cells, but are short-lived and cannot divide to reproduce themselves. The cells were designed to respond to a unique chemical signature on E. coli bacteria. They were able to detect, attack and destroy the bacteria in laboratory experiments.

Artificial cells previously only had been successful in nutrient-rich environments, Tan said. However, by optimizing the artificial cells’ membranes, cytosol and genetic circuits, the team made them work in a wide variety of environments with very limited resources such as water, emphasizing their robustness in less-than-ideal or changing conditions. These improvements significantly broaden the overall potential application of artificial cells.

Antibacterial artificial cells might one day be infused into patients to tackle infections resistant to other treatments. They might also be used to deliver drugs at the specific location and time, or as biosensors.

Learn more: Artificial Cells Are Tiny Bacteria Fighters



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