Not many microbe stories unrelated to Covid-19 made headlines in 2020, but one that did involved an announcement in autumn by biochemists at the University of Portsmouth, who used an enzyme from a rubbish-dwelling bacterium that lives on a diet of plastic bottles to create a ‘cocktail’ capable of breaking down PET bottles at industrial speeds. Meanwhile, in March 2020, German scientists identified a strain of bacteria that feeds happily on polyurethane, a plastic that is generally resistant to biodegradation.
The reason an organism becomes capable of digesting modern polluting scourges such as plastic is just chemistry and evolution. Many plastics are derived from natural organic materials such as hydrocarbons or cellulose, making it likely that something somewhere will find a way to exploit them as an energy source. That link between evolutionary chemistry and life forms (plants as well as microbes) underpins bioremediation – the use of natural organisms to provide an eco-friendly approach to clearing up pollutants ranging from toxic metals and oil to TNT and chemical weapons.
It’s an approach that already has precedent. There are marine microbes that digest oil and use it as an energy source, thanks to the fact that there are vents in the seabed where the black stuff has been bubbling out for millions of years. Oil-guzzling bacteria have been deployed to clean up several oil spills, including one off the coast of Kuwait during the Gulf War of 1991 and the Prestige spill near Spain in 2002. In the aftermath of the disastrous 2010 Deepwater Horizon oil rig explosion in the Gulf of Mexico, scientists observed an explosion in the local population of bacteria that wolfed down methane, known as methanotrophs. On land, meanwhile, bacteria found living in petroleum sludge at Iranian oil refineries have proved to be an eco-friendly way to treat contamination by petroleum hydrocarbons.
While bioremediation ticks many virtuous boxes, its genesis came out of conflict. When US armed forces began fighting in Korea during the early 1950s, scientist Howard Worne was commissioned to look at degradation of uniforms in the moist, humid climate. During his research, he discovered a microorganism that broke down fabrics previously thought to be non-biodegradable. Intrigued, Worne went on to isolate an organism capable of degrading phenols – still a common and highly toxic pollutant in industrial wastewater.
While various microbes have since been discovered that remove phenols, even better results have been obtained using certain forms of algae – a type of bioremediation called phycoremediation. The benefits of this approach were summed up in a 2018 study by a team at the National Institute of Technology in Durgapur, India: ‘The advantages of algae-based treatment include cost-effectiveness, low energy requirement, reduction in sludge formation and production of algal biomass. Algae biofuel is non-toxic, contains no sulphur and is highly biodegradable.’
This combination of decontamination with the creation of a useful byproduct exemplifies an approach that chimes well with a particular 21st-century ethos. ‘There is a lot of emphasis today toward low-carbon bioremediation and closing the loop of organic waste – referring to the circular economy defined by the Ellen MacArthur Foundation,’ says Frederic Coulon, professor of environmental chemistry and microbiology at Cranfield University in Bedforshire.
Circular-economy approaches seek to ‘design-out’ waste and pollution by keeping materials in use in order to support and regenerate natural systems. Bioremediation offers another good example of this philosophy with the use of waste fish bones to decontaminate soil laced with lead – a neurotoxin that continues to cause particular harm to child development worldwide. Like other bones, fish bone largely consists of calcium and phosphate. Ground up and blended into contaminated soil, phosphates freed as the bone decomposes migrate through the soil and bind with the toxic metal to create microscopic particles of pyromorphite, a stable crystalline mineral that can’t be absorbed by humans. Organisations such as the US military have regularly used fish-bone bioremediation to clean up lead-contaminated firing ranges. A 2005 US Defense Department report highlighted the vast savings of this approach compared to other options, citing a cost of US$22 per square yard (0.83 square metres) versus $104 for the next-cheapest method and $475 for the most expensive. All this without changing the soil’s permeability, porosity or density. According to the report, fish-bone bioremediation was ‘inexpensive, fast, long-lasting, and [didn’t] generate any hazard or environmental problem.’
In 2011, a pioneering civilian bioremediation project made safe heavily lead-contaminated soil around hundreds of homes in Oakland, California. Tilling ground up fish bone into the soil reduced lead levels by half within a few weeks, while providing work to dozens of previously unemployed locals. ‘A poisoned neighbourhood... become safer for children and a project that will revitalize yards and gardens, and employ local workers,’ wrote Suzanne Bohan in a piece for the Phys.org website. All thanks to waste from a local processor of pollock into fish sticks.
Surprisingly, the discovery of fish bone bioremediation came from fossils that date back aeons. As a graduate geology student at Oregon State University, Judith Wright discovered that the bones of tiny animals called conodonts – which flourished for 300 million years – were full of heavy metals that had been taken up after death, then stabilised and rendered harmless. A groundfish- bone product Wright developed – trademarked as Apatite II – has since helped to decontaminate soil and water not just of lead, but also copper, cadmium, zinc, plutonium, uranium, TNT and perchlorate, in sites ranging from old mines to military bases.
TURNING TO THE PLANT WORLD
It’s not just microbes and waste bones that can prove useful. Plants underpin another type of bioremediation known as phytoremediation. Semi-aquatic plants such as water hyacinth and duckweed have been known to draw up toxic metals, including lead and cadmium, from contaminated waters since observations made in Russia at the dawn of the nuclear age in the 1950s. And the fact that plants such as the wild herb Alpine pennycress thrive on zinc- and nickel-rich soils has helped prospectors in the Alps and Rocky Mountains find ore deposits.
In a 2004 paper, a team of scientists from Bulgaria, Belgium, Switzerland and the USA highlighted the existence of more than 400 plant species, found on all continents, in both temperate and tropical environments, that are metal accumulators. Increasing knowledge of phytoremediation has now seen Indian mustard pitted against lead, sunflowers against uranium and bulrush against selenium. Metal-accumulating plants also offer potential green remuneration thanks to a process called phytoextraction. This refers to the ability of some plants to draw metals from the soil and concentrate them in harvestable parts above ground, where they can be easily removed, dried and turned into metal-rich ash. The process has been dubbed phyto-mining – an apt tag given that ashes of pennycress grown on soil with a high zinc level can yield up to 40 per cent zinc, which is as good as high-grade ore. Other metals that could one day be mined by sinking roots into the ground rather than pit shafts are nickel and cobalt.
Of course, there are caveats. ‘Certain “contaminants” have value as a resource – such as metals – but this value is not easily realisable due to their dispersion and form in the environment,’ points out Mike Harbottle, senior lecturer in geoenvironmental engineering at Cardiff University. But for him, phytoremediation could still provide a novel, environmentally friendly opportunity not only ‘to extract the resource to help offset remedial costs, but also to help limit leakage from a circular economy’.
One of the most resonant phytoremediation projects took place in 1993 at the Pig’s Eye landfill in St Paul, Minnesota, a site so heavily contaminated with cadmium and zinc that it was illegal to visit without special permission. At this unpromising location, art and science came together in a conceptual-art project entitled ‘Revival Fields’. With scientific input from phytoremediation researcher Rufus Chaney, artist Mel Chin planted maize, ‘Merlin’ red fescue, bladder campion, Alpine pennycress and lettuce in a structured pattern. As the plants grew, not only did they slash levels of cadmium and zinc in the soil, but they also created a sculpted bioremediated ecological oasis amid a toxic wasteland. ‘There is this poetic idea that there is something dead, and through this process it becomes alive again,’ is how Chin described it.
Plants may develop a liking for metal in their diet because its presence in their stems and leaves protects them against certain fungal diseases and chewing insects. While many plants produce molecules that bind metals for storage, the most metal-loving hyperaccumulators also use organic acids that enable them to bind much greater amounts of the metals – like a form of boosted chemical defence.
Fungi are also in on the act (Geographical discussed some aspects of this in the June 2020 feature ‘The Future is Fungi’). In a 2008 TED talk entitled ‘6 Ways Fungi Can Save the World’, mycologist Paul Stamets highlighted their power to transform environments. Stamets described the vast network of fungal mycelium – the vegetative part of a fungus, consisting of a mass of branching, thread-like hyphae – in the soil as ‘the grand molecular disassemblers of nature’. So it’s perhaps not surprising that some fungi turn out to be pretty good at breaking down a range of pollutants, including plastics, explosives and radioactive metals. In one study, white rot fungus degraded around 95 per cent of TNT in the soil at a particular site.
Given the huge potential for using microbes and plants as an eco-friendly way to deal with a vast range of pollutants, why aren’t we seeing bacteria chowing down on plastic bottles or mushrooms sprouting from toxic soils everywhere we look?
Eric Grace’s 2006 book Biotechnology Unzipped: Promises and Realities outlines some of the reasons for the gap between the potential and a more widespread take-up of bioremediation as the principal go-to for industrial-decontamination operations. Simply put, for many organisations charged with clean-up duties there remains too much unpredictability as to how different bacteria or plants will work in a particular environment, which depends on factors such as the climate, soil conditions and the presence of other chemicals and organisms. ‘It’s not just the remedial method and the contaminant that are important – the environment is key,’ says Cardiff University’s Harbottle. ‘Techniques that work on one site won’t work on another because of the soil type, the groundwater pH or any number of other myriad parameters. A single plant couldn’t be expected to solve all problems with one contaminant, as the environment will govern the ability of the plant to behave in that way.’ However, just because multiple forms of bioremediation may have to be applied to different sites hardly seems a genuine hurdle.
There also remain whole avenues of bioremediation that are under researched. One is pioneering work carried out by Morrie Craig, a professor at Oregon State University during the 1990s on the relative tolerance of Alaska’s bowhead whales to shamefully high levels of oil and other industrial pollutants in their food chain. Craig found that the leviathans possessed bacteria in their gut that could break down oil carcinogens such as napthalene and anthracene, as well as PCBs (polychlorinated biphenyls). Furthermore, the whales’ gut bacteria proved to be anaerobic, capable of converting the pollutants into non-toxic substances in the absence of oxygen – a highly useful trait in many polluted soils.
Favouring old approaches to pollutants – be it incineration or merely shifting the problem elsewhere through giant, toxic landfills – flies in the face of modern views about the benefits of both eco-friendly approaches and circular economies. It’s time, perhaps, to turn to a truly 21st-century way to deal with the scourge of pollution.