Diesel oil floating on the ocean’s surface, old chemical hazards stacked up in an industrial warehouse, pollutants filtrating into the soil… Industrial activities produce a vast amount of residues that are a risk not only for humans, but for the environment. These compounds are often hard to clean and end up in places that are difficult to reach, so getting rid of them by hand is not always an option. However, bacteria could help.
Designing microbes that “eat” the pollutant is an approach that is on the rise among scientists that work in bioremediation: using biology to clean up waste. Bacteria and other microorganisms already munch on different molecules to obtain energy, so the key here is to make them eat the pollutant. Developing & tailoring such microorganisms is possible thanks to the advances in synthetic biology. And in this post, we want to show you how researchers build pollutant-eating bacteria in three steps.
Step 1: Know the enemy
The first step is identifying the toxic compound. It’s not the same an oil spill (which more likely is a mix of various complex molecules) than a specific residue from an industrial process. The compounds differ, and so they will have to be degraded through different reactions. In the case of bacteria, these reactions are called metabolic pathways and the key players in them are enzymes: special proteins that modify other molecules, sometimes fostering their degradation. The goal is to identify which enzymes cause the reactions, to exploit this metabolic route in the microorganism where we have identified this property. Another option is to take this genetic information away and insert it in a modified microorganism that could host and produce these molecules.
To know how the compound can be degraded, what enzymes are necessary for the reactions to happen, and what the resulting materials are, scientists use publicly available databases that contain multitude of reactions. There are multiple of them: EAWAG-BBD, envipath, MetaCyc, BioCyc…
On them, scientists can enter the problematic compound, find the metabolic pathways that have it as a starting point and look where these pathways end up. Mind you, not every pathway is valid. Since the goal is to engineer bacteria that eat the pollutant, these pathways have to end in a molecule that the bacteria find useful and gives them energy, so they can munch on it.
What if it’s impossible to find a metabolic pathway for the compound? Or if it is man-made and therefore there is no naturally occurring pathways that can take care of it? Computational methods have developed so much in the last decades that they allow to predict possible enzymes and pathways that can degrade it. These predictions are a huge time-saver, facilitating the first steps towards a viable option.
Step 2: Choose a powerful ally
Once that a viable reaction is found, it’s time to find a host: a bacterium that will have a metabolism close to the chain of reactions that get rid of the pollutant. And it’s not an easy choice.
Although bacteria have things in common, each one thrives in different conditions and has different weaknesses. Maybe one is easier to cultivate, but the other has a genome easier to edit. Or maybe another one thrives in the harsh environment it is supposed to work in, so it’s a good candidate just because it will survive. In real life, researchers weight carefully the options before deciding and there’s no standard response. What usually happens is that the best option is to choose the organism that already does something resembling the objective. If there’s bacteria that eats away a molecule similar to the pollutant, usually that’s the best shot researchers can get.
Step 3: Get the right weapon
If the bacteria present on the environment were able to process the residue in the first place, it wouldn’t be a problem: they’d get rid of the pollutant and that’s all. But bacteria don’t usually do that. They need a little help from researchers. It’s time to put steps 1 and 2 together: making the chosen host produce the enzymes identified in step 1, so it can eat away the pollutant. And how do researchers do that? Thanks to the genetic tools refined in the last decades, researchers can pinpoint the pieces of the genome responsible for producing the specific enzyme in an organism, extract them and insert them in the host. Voilà! The organism now will produce the enzymes and much on the pollutant.
Except reality isn’t always that simple. Sometimes the host doesn’t produce the enzymes. Other times one of the enzymes of the reaction is toxic for the host, so it dies producing it. Researchers can even have the perfect host, producing the right enzymes… but it doesn’t eat the pollutant because it is eating more conventional food. Kind of like trying to make you eat a salad, when you have a delicious burger in front of you. The complications are always there.
Following these steps, at Rafts4biotech we have been able to make advances with bacteria that can degrade TCP (an industrial residue). Other researchers have been exploring bacteria that could help us degrade nuclear waste, and some microorganisms helped get rid of the oil during the Deepwater Horizons spill. All the details are available on our paper on the matter. Bioremediation is not science fiction anymore!
Sadly, bacteria are not cleaning our houses. Yet.