A bug’s life: Could bacteria help us clean up our mess?

May 20, 2023 02:45 PM IST

They’re an army of superheroes, in land, sea and air. Some can act as bio-batteries. Others digest plastic. Some emit energy, simply by breathing.

There’s a type of bacteria that can build a metal suit for itself out of toxic cobalt; it’s been nicknamed Iron-Man. Another can turn plastic waste into biodegradable polymers, essentially making alternatives to plastic from plastic. Still others can act as bio-batteries, emitting electric energy through filaments as they breathe.

(Images: Wikimedia Commons; Imaging: Puneet Kumar) PREMIUM
(Images: Wikimedia Commons; Imaging: Puneet Kumar)

Amid the climate crisis and intensifying resource stresses, could these and other newly discovered superpowers help us clean up our mess?

Bacteria have been keeping house since the days when Earth was still covered in lava, billions of years ago. They processed noxious gasses to help make the planet habitable.

They are no magic cures, though. “Working with bacteria takes time and patience, especially since certain toxic chemicals can affect bacterial growth and impair their function,” says Mukesh Doble, a bacteria-use researcher and retired professor of biotechnology at the Indian Institute of Technology, Madras (IIT-M).

But “microbes have a huge role to play in how we can fight climate change,” says Steven Allison, professor of ecology and evolutionary biology at University of California, Irvine.

Since 2018, for instance, chemical manufacturer LanzaTech has run a production plant that uses bacteria derived from rabbit faeces to turn waste gas from steel mills (a mix of carbon monoxide, carbon dioxide and hydrogen) into ethanol for use in cars. Eventually, the aim is to use it in aircraft.

Richard Branson’s Virgin Atlantic has been working with LanzaTech since 2011, according to a 2016 post by Branson, to produce jet fuel from such gasses.

“Companies such as LanzaTech, Loam and Pivot Bio are developing microbe-powered products as commercial solutions to reduce carbon footprints,” says Nguyen K Nguyen, director of the American Academy of Microbiology.

Today’s research with bacteria is a reminder to be creative and not limited in how we view the possibilities, says Gemma Reguera, a professor of microbiology and molecular genetics at Michigan State University.

Reguera was part of the team that discovered Geobacter’s Iron-Man properties, in 2020. “Research is the freedom to explore, to search and search and search,” she says. “We have textbook opinions about what microbes can and should do, but life is so diverse and colourful. There are other processes out there waiting to be discovered.”

Some already have. Take a look.

Suiting up

The “Iron-Man” bacteria has been nicknamed for its ability to survive exposure to toxic cobalt by essentially building a metal suit for itself from that element. It’s an ability discovered by researchers at Michigan State University in 2020.

Cobalt is a valuable but increasingly scarce metal used in batteries for electric vehicles and alloys for spacecraft. It is highly toxic to living things, including humans and bacteria.

The research team, in their study, detail how Geobacter sulfurreducens essentially mines cobalt from minerals and metal oxides in its environment, and wraps itself in the cobalt, to keep the metal from penetrating its cells and poisoning it. Even high levels of cobalt exposure failed to make a dent in the suit. Microscope images showed the microbes shrouding themselves in the metal and thriving, says Gemma Reguera, who was part of the research team.

This ability means that the bacteria could be used to extract cobalt from discarded lithium-ion batteries, for reuse or at least a more sustainable form of e-waste disposal. Researchers now plan to test whether Geobacter can absorb other toxic metals, specifically cadmium, which is also prevalent in e-waste.

“The lesson is that we really need to think outside the box, especially in biology,” Reguera says. “We just know the tip of the iceberg. Microbes have been on earth for billions of years, and to think that they can’t do something precludes us from so many ideas and applications.”

Life in plastic

In the race to find a bacteria that can quickly and efficiently consume plastic, Rhodococcus ruber has emerged a front-runner. It breasted the tape in January, when a study showed that it can eat and digest plastic, rather than merely degrading it, as other bacteria have been shown to do.

Researchers from the Royal Netherlands Institute for Sea Research also identified the enzymes responsible for this ability, which could lead to the development of new biodegradation technologies.

Their study suggests that Rhodococcus ruber can break down about 1% of fed plastic a year into carbon dioxide and other non-toxic substances. “This is certainly not a solution to the problem of the plastic soup in our oceans,” researchers emphasised in a statement. The experiments are mainly proof of principle, “one piece of the jigsaw”.

Meanwhile, at Northwestern University, researchers have identified a species with a diverse range of metabolic pathways that allows it to consume certain compounds in plastic, and turn them into biodegradable polymers.

A study published in Nature Chemical Biology in February demonstrated that Comamonas testosteroni can degrade certain compounds released from the breakdown of polyethylene terephthalate, which is used widely in disposable food containers and packaging materials.

There is need for further study on how the polymers produced by the bacteria can be used. “But these polymers can be used as a precursor to plastics, so you can basically potentially use plastics to make new plastics,” says Ludmilla Aristilde, associate professor of civil and environmental engineering at Northwestern’s McCormick School of Engineering, and lead author of the study.

Arctic explorers

We’ve known for a while that as global temperatures soar, melting Arctic permafrost is releasing an alarming amount of methane — a greenhouse gas 25% more potent than carbon dioxide — into the atmosphere. A study published in March 2020 has discovered a type of methane-oxidising bacteria that lives in upland Arctic soils that may be able to offset some of these emissions.

The study, led by researchers at Purdue University, suggests that net greenhouse gas emissions from the Arctic may be much lower than previously estimated, due to increased productivity of a type of bacteria known as high affinity methanotrophs, or HAMs.

On average, methanotrophic bacteria consume between 25 and 130 million metric tonnes of methane per year, says a study published in the journal Nature in 2018, and have captivated researchers for their natural ability to oxidise the potent greenhouse gas and convert it into the green, sustainable fuel methanol.

For years, little was known about how the complex reaction occurs. Now, findings from Northwestern University, published in March 2022 in the journal Science, throw light on the enzyme that the bacteria uses to catalyse the reaction.

Current industrial processes to catalyse a methane-to-methanol reaction require tremendous pressure and extreme temperatures of over 1,300 degrees Celsius. Methanotrophs perform the reaction at room temperature and for free, this study notes. Once the process has been decoded, could humans replicate it?

“Methane has a very strong bond, so it’s pretty remarkable that there’s an enzyme that can do this,” Amy Rosenzweig, professor of molecular biosciences at Northwestern and senior author of the paper, said in a statement.

An oily agent

A rod-shaped bacteria commonly found in soil is astonishing scientists with its appetite for hydrocarbons.

“Bacillus subtilis, which is a good bacteria that has been used as a probiotic to improve gut health, can produce enzymes that break down complex hydrocarbons in oil into simpler compounds — smaller bubbles, essentially — making it easier for other microorganisms to feed on the oils,” says Mukesh Doble, a bacteria-use researcher and retired professor of biotechnology at the Indian Institute of Technology, Madras (IIT-M).

Bacillus subtilis could potentially help purify impure oil; break down industrial waste; even clean up oil spills. A study conducted at IIT-M, published in the journal Energy Sources Part A: Recovery, Utilization, and Environmental Effects in 2016, found that Bacillus subtilis succeeded in degrading samples of crude oil by up to 80% within 10 days, a process that usually takes a group of bacteria weeks or months.

“The beauty is, you don’t need to genetically modify this bacteria,” Doble says. To help it get a head start, all it needs is a little glucose as a nutrient source, after which it will slowly adapt and look for carbon sources of its own accord; in oil, this search leads it to break down hydrocarbons.”

One constraint is that it does not fare well amid contamination by other microorganisms, including unwanted strains of Bacillus subtilis. Contamination control measures will be crucial to any eventual use of this bacteria in industrial processes. Another thing to watch out for would be mutations over time, which could affect efficacy and performance, Doble says.

Carbon guzzler

Perhaps the cleanest way to rapidly draw carbon dioxide out of the air is by feeding it to cyanobacteria, a study published in Renewable and Sustainable Energy Reviews in 2022 suggests. This bacteria acts fast and does not produce toxic effluents in the process. Instead, it converts carbon dioxide into oxygen and biological components that can be used to make biofuels and feedstock.

Another study published in Environmental Science & Technology in 2018 estimates that, globally, cyanobacteria and other phytoplankton already likely sequester up to 1.5 billion tonnes of carbon each year through photosynthesis in the oceans.

The challenge with using cyanobacteria for large-scale industrial application is the development of cost-effective and scalable cultivation technologies. Also, researchers say, different strains vary in growth rate, biomass production and capabilities for producing desired compounds, making consistent results a challenge.

Bacteria can’t work miracles, but we’re at the point where every bit counts.

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