Scientists create strain of bacteria that consumes carbon dioxide

Researchers have engineered Escherichia coli bacteria to make energy exclusively from carbon dioxide, according to a paper published November 27 in Cell.

E. coli are normally heterotrophs—organisms that get their energy sources from ingesting organic compounds, such as glucose—but the new study shows that they can be turned into autotrophs, making their own energy by turning carbon dioxide from the atmosphere into biomass.

“I find it fundamentally amazing that an organism which evolved over billions of years to live a heterotrophic lifestyle can so quickly and completely change into an autotroph,” Dave Savage, a biochemist at University of California, Berkeley, who was not involved with the study, tells The Scientist in an email. “It suggests that metabolism is extremely malleable.”

This process of using inorganic carbon to make biomass, called carbon fixation, could be used to solve “some of the biggest challenges of humanity today,” Ron Milo, a systems biologist at the Weizmann Institute of Science in Israel and the lead author of the paper, tells The Scientist. For example, increasing carbon fixation in plants generates more biomass, which could increase the world’s food supply.

The team set out to make E. coli—a “very genetically malleable model organism,” says Milo—fix carbon as a step toward sustainable industrial processes such as creating biofuel.

E. coli doesn’t normally have molecular mechanisms in place to use CO2, so the researchers gave it genes for the ability to fix carbon that were based on the gene sequence of carbon-fixing Pseudomonas bacteria. These changes weren’t enough to force the bacteria to switch to being autotrophic, so the team also disabled three genes involved in heterotrophic metabolism and put the bacteria into growth chambers with limited amounts of sugar, which starved them. In this environment, there was an advantage for bacteria that used CO2 instead of the finite sugar supply, and the researchers wanted to see if the bacteria could evolve to only use CO2.

The E. coli were grown on sodium formate, a carbon molecule that donates the necessary electrons during the process of making energy, but doesn’t contribute to biomass. The air in the growth chambers was also enriched with carbon dioxide.

After approximately 200 days, the bacteria relied completely on carbon dioxide from the air to generate biomass while taking in formate as a necessary ingredient for the chemical reactions. When the scientists analyzed the bacterial genome, they found that the bacteria evolved to use carbon dioxide as their energy source after as few as 11 mutations. Some of the changes occurred in genes related to carbon fixation, while others were in genes that are known to mutate in other lab evolution experiments or have no known role in energy production from CO2.


Heterotrophic E. coli (left) produce biomass from sugar, but lab-evolved autotrophic E. coli from the new study (center) use CO2 instead. The authors envision autotrophic E. coli that use renewable energy and have no net carbon emissions in the future (right).

“It’s a proof of concept for the field, that you can really rewire . . . the metabolic features of living organisms from scratch. It’s an exciting step forward,” Tobias Erb, a synthetic biologist at the Max Planck Institute for Terrestrial Microbiology in Germany who wrote a commentary on the study, tells The Scientist. However, “if the strain that they created [is] of biotechnological relevance in the future . . . I think is still up to debate,” he says.

For instance, the autotrophic E. coli currently produce more carbon dioxide as a byproduct than they take in. This could be solved by producing formate from carbon dioxide in the future, so that there are no net carbon dioxide emissions.

In addition, the researchers used high carbon dioxide levels in the bacteria’s growth chambers—around 10 percent of the air—but it’s only 0.04 percent of Earth’s atmosphere. “We’re interested to see if we could move it towards ambient carbon dioxide levels, meaning that one could use the ambient atmosphere that has much less [carbon dioxide], 400 parts per million,” says Milo.

“It’s an interesting concept now. Whether it actually is something that becomes useful in terms of application, that’s another question,” Patrik Jones, who studies microbial metabolic engineering at Imperial College London and was not involved with the study, tells The Scientist. “It’s definitely a step towards that direction . . . But then I think it’s important to realize that there are more steps needed in order to utilize this.”

ABOVE: FLICKR.COM, NIAID
Researchers have engineered Escherichia coli bacteria to make energy exclusively from carbon dioxide, according to a paper published today (November 27) in Cell.

E. coli are normally heterotrophs—organisms that get their energy sources from ingesting organic compounds, such as glucose—but the new study shows that they can be turned into autotrophs, making their own energy by turning carbon dioxide from the atmosphere into biomass.

“I find it fundamentally amazing that an organism which evolved over billions of years to live a heterotrophic lifestyle can so quickly and completely change into an autotroph,” Dave Savage, a biochemist at University of California, Berkeley, who was not involved with the study, tells The Scientist in an email. “It suggests that metabolism is extremely malleable.”

This process of using inorganic carbon to make biomass, called carbon fixation, could be used to solve “some of the biggest challenges of humanity today,” Ron Milo, a systems biologist at the Weizmann Institute of Science in Israel and the lead author of the paper, tells The Scientist. For example, increasing carbon fixation in plants generates more biomass, which could increase the world’s food supply.

The team set out to make E. coli—a “very genetically malleable model organism,” says Milo—fix carbon as a step toward sustainable industrial processes such as creating biofuel.

E. coli doesn’t normally have molecular mechanisms in place to use CO2, so the researchers gave it genes for the ability to fix carbon that were based on the gene sequence of carbon-fixing Pseudomonas bacteria. These changes weren’t enough to force the bacteria to switch to being autotrophic, so the team also disabled three genes involved in heterotrophic metabolism and put the bacteria into growth chambers with limited amounts of sugar, which starved them. In this environment, there was an advantage for bacteria that used CO2 instead of the finite sugar supply, and the researchers wanted to see if the bacteria could evolve to only use CO2.

The E. coli were grown on sodium formate, a carbon molecule that donates the necessary electrons during the process of making energy, but doesn’t contribute to biomass. The air in the growth chambers was also enriched with carbon dioxide.

After approximately 200 days, the bacteria relied completely on carbon dioxide from the air to generate biomass while taking in formate as a necessary ingredient for the chemical reactions. When the scientists analyzed the bacterial genome, they found that the bacteria evolved to use carbon dioxide as their energy source after as few as 11 mutations. Some of the changes occurred in genes related to carbon fixation, while others were in genes that are known to mutate in other lab evolution experiments or have no known role in energy production from CO2.

Heterotrophic E. coli (left) produce biomass from sugar, but lab-evolved autotrophic E. coli from the new study (center) use CO2 instead. The authors envision autotrophic E. coli that use renewable energy and have no net carbon emissions in the future (right).
GLEIZER ET AL.
“It’s a proof of concept for the field, that you can really rewire . . . the metabolic features of living organisms from scratch. It’s an exciting step forward,” Tobias Erb, a synthetic biologist at the Max Planck Institute for Terrestrial Microbiology in Germany who wrote a commentary on the study, tells The Scientist. However, “if the strain that they created [is] of biotechnological relevance in the future . . . I think is still up to debate,” he says.

For instance, the autotrophic E. coli currently produce more carbon dioxide as a byproduct than they take in. This could be solved by producing formate from carbon dioxide in the future, so that there are no net carbon dioxide emissions.

In addition, the researchers used high carbon dioxide levels in the bacteria’s growth chambers—around 10 percent of the air—but it’s only 0.04 percent of Earth’s atmosphere. “We’re interested to see if we could move it towards ambient carbon dioxide levels, meaning that one could use the ambient atmosphere that has much less [carbon dioxide], 400 parts per million,” says Milo.

“It’s an interesting concept now. Whether it actually is something that becomes useful in terms of application, that’s another question,” Patrik Jones, who studies microbial metabolic engineering at Imperial College London and was not involved with the study, tells The Scientist. “It’s definitely a step towards that direction . . . But then I think it’s important to realize that there are more steps needed in order to utilize this.”

Emily Makowski is an intern at The Scientist. Email her at emakowski@the-scientist.com.

https://www.the-scientist.com/news-opinion/lab-evolved-e–coli-makes-energy-solely-from-carbon-dioxide-66788?utm_campaign=TS_DAILY%20NEWSLETTER_2019&utm_source=hs_email&utm_medium=email&utm_content=80070748&_hsenc=p2ANqtz-_mk5jB1Vyqx3xPsKPzk1WcGdxEqSmuirpfpluu4Opm4tMO6n7rXROJrCvQp0yKBw2eCo4R4TZ422Hk6FcfJ7tDWkMpyg&_hsmi=80070748

Seaweed helps trap carbon dioxide in sediment

Every beachgoer can spot seaweed in the ocean or piling up on the beach, but Florida State University researchers working with colleagues in the United Kingdom have found that these slimy macroalgae play an important role in permanently removing carbon dioxide from the atmosphere.

Their work is published in the journal Ecological Monographs by the Ecological Society of America.

The researchers, who partnered with ecologists from Plymouth Marine Laboratory in the United Kingdom, investigated how seaweed absorbed carbon and processed it, trapping it in the seafloor.

“Seaweeds have been ignored in the ‘blue carbon’ storage literature in favor of seagrasses and mangroves, which physically trap carbon from sediments and their own biomass in root structures,” said Assistant Professor of Biological Science Sophie McCoy. “Macroalgae are also often overlooked by oceanographers who study the carbon cycle, as their high productivity occurs close to shore and has been thought to stay and cycle locally.”

In designing the study, researchers suspected that the high productivity and huge amount of seasonal biomass of annual algae would provide carbon subsidies farther offshore than typically considered, and that these subsidies would be important to benthic food webs there.

That was exactly what they found. They also discovered that this was the process that leads to the burial of seaweed carbon in ocean sediments.

Blue carbon is the carbon captured in marine systems both through photosynthesis and then by trapping it in the seafloor. Researchers sequenced environmental DNA and modeled stable isotope data for over a year off the coast of Plymouth, England. Through this, they found that seaweed debris was an important part of the food web for marine organisms and that much of that debris was ultimately stored in sediments or entered the food web on the seafloor.

Jeroen Ingels, a researcher at the FSU Coastal and Marine Laboratory who conducted the meiofauna work for the study, said the research not only explains seaweed’s role in the food web, but it also shows that human activities that affect seaweed and the sea floor are important to monitor.

“The human activities that are impacting macroalgae and sediment habitats and their interstitial animals are undermining the potential for these systems to mitigate climate change by affecting their potential to take up and cycle carbon,” he said. “The study really illustrates in a new way how seaweed and subsequently benthic animals can contribute in a significant way to blue carbon.”

The team found that about 8.75 grams of macroalgae carbon are trapped per square meter of sediment each year.

Ana M. Queiros, a scientist at Plymouth Marine Laboratory and the paper’s lead author, said these first measurements of seaweed carbon trapped in the sediment gives scientists more information to help them develop sustainable environmental practices.

“They tell us that the global extent of blue carbon-meaningful marine habitats could be much wider than we previously thought,” she said. “Identifying these areas and promoting their management will let us capitalize on the full potential of the ocean’s blue carbon towards the stabilization of the global climate system.”

Journal Reference:

Ana Moura Queirós, Nicholas Stephens, Stephen Widdicombe, Karen Tait, Sophie J. McCoy, Jeroen Ingels, Saskia Rühl, Ruth Airs, Amanda Beesley, Giorgia Carnovale, Pierre Cazenave, Sarah Dashfield, Er Hua, Mark Jones, Penelope Lindeque, Caroline L. McNeill, Joana Nunes, Helen Parry, Christine Pascoe, Claire Widdicombe, Tim Smyth, Angus Atkinson, Dorte Krause‐Jensen, Paul J. Somerfield. Connected macroalgal‐sediment systems: blue carbon and food webs in the deep coastal ocean. Ecological Monographs, 2019; e01366 DOI: 10.1002/ecm.1366

https://www.sciencedaily.com/releases/2019/06/190603124721.htm

Thanks to Lynn and Bill Penland for bringing this to the It’s Interesting community.

Chemists make first-ever ring of pure 18-atom ‘cyclocarbon’ that could be a step towards molecule-scale transistors

by Davide Castelvecchi

Long after most chemists had given up trying, a team of researchers has synthesized the first ring-shaped molecule of pure carbon — a circle of 18 atoms.

The chemists started with a triangular molecule of carbon and oxygen, which they manipulated with electric currents to create the carbon-18 ring. Initial studies of the properties of the molecule, called a cyclocarbon, suggest that it acts as a semiconductor, which could make similar straight carbon chains useful as molecular-scale electronic components.

It is an “absolutely stunning work” that opens up a new field of investigation, says Yoshito Tobe, a chemist at Osaka University in Japan. “Many scientists, including myself, have tried to capture cyclocarbons and determine their molecular structures, but in vain,” Tobe says. The results appear in Science1 on 15 August.

Pure carbon comes in several different forms, including diamond, graphite and ‘nanotubes’. Atoms of the element can form chemical bonds with themselves in various configurations: for example, each atom can bind to four neighbours in a pyramid-shaped pattern, as in diamond; or to three, as in the hexagonal patterns that make up the single-atom-thick sheets of graphene. (Such a three-bond pattern is also found in bulk graphite as well as in carbon nanotubes and in the globular molecules called fullerenes.)

But carbon can also form bonds with just two nearby atoms. Nobel-prizewinning chemist Roald Hoffmann at Cornell University in Ithaca, New York, and others have long theorized that this would lead to pure chains of carbon atoms. Each atom might form either a double bond on each side — meaning the adjacent atoms share two electrons — or a triple bond on one side and a single bond on the other. Various teams have attempted to synthesize rings or chains based on this pattern.

But because this type of structure is more chemically reactive than graphene or diamond, it is less stable, especially when bent, says chemist Przemyslaw Gawel of the University of Oxford, UK. Synthesizing stable chains and rings has usually required the inclusion of elements other than carbon. Some experiments have hinted at the creation of all-carbon rings in a gas cloud, but they have not able to find conclusive proof.

One ring
Gawel and his collaborators have now created and imaged the long-sought ring molecule carbon-18. Using standard ‘wet’ chemistry, his collaborator Lorel Scriven, an Oxford chemist, first synthesized molecules that included four-carbon squares coming off the ring with oxygen atoms attached to squares. The team then sent their samples to IBM laboratories in Zurich, Switzerland, where collaborators put the oxygen–carbon molecules on a layer of sodium chloride, inside a high-vacuum chamber. They manipulated the rings one at a time with electric currents (using an atomic-force microscope that can also act as a scanning-tunelling microscope), to remove the extraneous, oxygen-containing parts. After much trial-and-error, micrograph scans revealed the 18-carbon structure. “I never thought I would see this,” says Scriven.

The IBM researchers showed that the 18-carbon rings had alternating triple and single bonds. Theoretical results had disagreed over whether carbon-18 would have this kind of structure, or one made entirely of double bonds.

Alternating bond types are interesting because they are supposed to give carbon chains and rings the properties of semiconductors. The results suggest that long, straight carbon chains might be semiconductors, too, Gawel says, which could make them useful as components of future molecular-sized transistors.

For now, the researchers are going to study the basic properties of carbon-18, which they have been able to make one molecule at a time only. They are also going to keep trying alternative techniques that might yield greater quantities. “This is so far very fundamental research,” Gawel says.

“The work is beautiful,” says Hoffmann, although he adds that it remains to be seen whether carbon-18 is stable when lifted off the salt surface, and whether it can be synthesized more efficiently than one molecule at a time.

doi: 10.1038/d41586-019-02473-z
References
1. Kaiser, K. et al. Science https://doi.org/10.1126/science.aay1914 (2019).

https://www.nature.com/articles/d41586-019-02473-z?utm_source=Nature+Briefing&utm_campaign=8838a84803-briefing-dy-20190819&utm_medium=email&utm_term=0_c9dfd39373-8838a84803-44039353

Soviet Union’s collapse led to massive drop in carbon emissions when people could not long afford meat-heavy diets.


A Soviet cow-fattening complex pictured in 1982.Credit: Nikolai Akimov/TASS

by Quirin Schiermeier

The collapse of the Soviet Union in 1991 led to a huge drop in greenhouse-gas emissions because the resulting economic crisis meant many people stopped eating meat.

Meat from domestic livestock farming was a main food staple during communist rule in the region. In 1990, Soviet citizens each consumed an average 32 kilograms of beef a year — 27% more than Western Europeans and four times more than the global average at the time.

But meat demand and livestock production in the region fell drastically when the prices of everyday consumer products soared and the purchasing power of the rouble dwindled in the post-communist economic crisis. An estimated one-third of late-Soviet cropland has been abandoned since.

These changes in the food and agriculture system in the former Soviet nations resulted in a net reduction of 7.6 billion tonnes of greenhouse gases in carbon dioxide equivalent from 1992 to 2011, researchers find from an analysis of data on livestock consumption and international trade1 (see ‘Soviet shocks’). The drop is equivalent to one-quarter of CO2 emissions from Amazon deforestation over the same period. Russia currently emits about 2.5 billion tonnes of greenhouse gases (CO2 equivalent) per year.

The figure considers emissions that result from domestic production of livestock and imported livestock, as well as carbon locked in soils and plants on abandoned Soviet cropland.

“There was a large drop in industrial production and emissions after the collapse of the Soviet Union, so it should be no surprise the same happened with food consumption and production,” says Glen Peters, a carbon-budget specialist at the Center for International Climate Research in Oslo, who was not involved in the analysis. “The study highlights the potential for carbon uptake in the former Soviet Union but also the risks to that carbon being released if agricultural production returns.”

Today, animal agriculture is responsible for 14.5% of human-caused greenhouse-gas emissions globally. Beef is the most emissions-intensive food because pastures are often created by clearing forests and savannahs.

Meat consumption — especially beef — and land-use changes in Russia and central Asia are a widely overlooked factor in calculations of greenhouse-gas emissions from land around the globe, says study author Florian Schierhorn at the Leibniz Institute of Agricultural Development in Transition Economies in Halle, Germany.

Trends in international trade suggest that emissions associated with meat consumption are on the rise again: Russia has over the past decade become a top destination for beef exported mainly from South America.

doi: 10.1038/d41586-019-02024-6

References
1. Schierhorn, F. et al. Environ. Res. Lett. 14, 065009 (2019).

https://www.nature.com/articles/d41586-019-02024-6?utm_source=Nature+Briefing&utm_campaign=34225bcef1-briefing-dy-20190701&utm_medium=email&utm_term=0_c9dfd39373-34225bcef1-44039353

Researchers find new phase of carbon, Q-carbon, that is brighter and harder than diamond and can be made easily and inexpensively in less than a second.

Researchers from North Carolina State University have discovered a new phase of solid carbon, called Q-carbon, which is distinct from the known phases of graphite and diamond. They have also developed a technique for using Q-carbon to make diamond-related structures at room temperature and at ambient atmospheric pressure in air.

Phases are distinct forms of the same material. Graphite is one of the solid phases of carbon; diamond is another.

“We’ve now created a third solid phase of carbon,” says Jay Narayan, the John C. Fan Distinguished Chair Professor of Materials Science and Engineering at NC State and lead author of three papers describing the work. “The only place it may be found in the natural world would be possibly in the core of some planets.”

Q-carbon has some unusual characteristics. For one thing, it is ferromagnetic – which other solid forms of carbon are not.

“We didn’t even think that was possible,” Narayan says.

In addition, Q-carbon is harder than diamond, and glows when exposed to even low levels of energy.
“Q-carbon’s strength and low work-function – its willingness to release electrons – make it very promising for developing new electronic display technologies,” Narayan says.

But Q-carbon can also be used to create a variety of single-crystal diamond objects. To understand that, you have to understand the process for creating Q-carbon.

Researchers start with a substrate, such as sapphire, glass or a plastic polymer. The substrate is then coated with amorphous carbon – elemental carbon that, unlike graphite or diamond, does not have a regular, well-defined crystalline structure. The carbon is then hit with a single laser pulse lasting approximately 200 nanoseconds. During this pulse, the temperature of the carbon is raised to 4,000 Kelvin (or around 3,727 degrees Celsius) and then rapidly cooled. This operation takes place at one atmosphere – the same pressure as the surrounding air.

The end result is a film of Q-carbon, and researchers can control the process to make films between 20 nanometers and 500 nanometers thick.

By using different substrates and changing the duration of the laser pulse, the researchers can also control how quickly the carbon cools. By changing the rate of cooling, they are able to create diamond structures within the Q-carbon.

“We can create diamond nanoneedles or microneedles, nanodots, or large-area diamond films, with applications for drug delivery, industrial processes and for creating high-temperature switches and power electronics,” Narayan says. “These diamond objects have a single-crystalline structure, making them stronger than polycrystalline materials. And it is all done at room temperature and at ambient atmosphere – we’re basically using a laser like the ones used for laser eye surgery. So, not only does this allow us to develop new applications, but the process itself is relatively inexpensive.”
And, if researchers want to convert more of the Q-carbon to diamond, they can simply repeat the laser-pulse/cooling process.

If Q-carbon is harder than diamond, why would someone want to make diamond nanodots instead of Q-carbon ones? Because we still have a lot to learn about this new material.

“We can make Q-carbon films, and we’re learning its properties, but we are still in the early stages of understanding how to manipulate it,” Narayan says. “We know a lot about diamond, so we can make diamond nanodots. We don’t yet know how to make Q-carbon nanodots or microneedles. That’s something we’re working on.”

NC State has filed two provisional patents on the Q-carbon and diamond creation techniques.
The work is described in two papers, both of which were co-authored by NC State Ph.D. student Anagh Bhaumik. “Novel Phase of Carbon, Ferromagnetism and Conversion into Diamond” will be published online Nov. 30 in the Journal of Applied Physics. “Direct conversion of amorphous carbon into diamond at ambient pressures and temperatures in air” was published Oct. 7 in the journal APL Materials.