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Phytoremedi…what? Or the art of tackling soil diversity to decontaminate soils

by Sara Correa Garcia

Some weeks ago, I attended this mingling event where the excuse for meeting new people is improving your level in a given language X.  You know how this works. It is pretty similar to any romantic date. You have a set of pre-made questions to start the conversation. Among the most common, we found the well-known: what do you do in life? And all the other work-related versions of this question. Every time someone asks something like this to us, PhD students, we either:

1) have an excessively intricate paragraph-like sentence to drop, or
2) answer with the explain-to-a-five-year-old short punching catchphrase.

Using one strategy or the other depends on different factors. Do we feel like engaging in a deeper conversation about our project with the person in front of us? Do we want to attract that person (potential collaborators or founders, anyone)? Or do we just want to go back home, because we don’t know what we are doing anymore?

I found myself using the complicated version more often than I would like to admit, so my interlocutor nods and walks away slowly.

As PhD students struggling with our experiments, we don’t always want to talk about our PhD life, especially when for the last month all lab work we attempted seems to fail. However, since I have recently succeeded in my 3rd year project evaluation, I felt confident about engaging in an “explain-to-a-five-year-old” conversation about my research. So, when asked during the language meeting, I literally answered:
– I work on phytoremediation, or the art of using plants and their micro-sized superheroes that inhabit the roots to fight against the villain oil pollution.

The person in front of me squinted, slightly turned his head, opened his mouth in an utterly confusion gesture and said: 

– Wait, phytoremedi…what? Superheroes, though?
Obviously, the message was missed on my too risky Marvel reference. 

Apparently, this kind of reference is well received if, and only if, the interlocutor is effectively 5 years old. The embarrassment rush quickly mounted my face, but clearly, I got his attention, then it was only a matter of developing from here.  At that moment, though, I was overwhelmed from the awkwardness I had just created and I lacked a proper continuation, so I just asked the question back and ended the conversation as soon as I could. Later, while commuting back home, I had this whole planned answer speeding in my head.
In order to save myself from another embarrassing moment in the near future when interacting with non-scientist grown-ups, I wrote this improved explanation for what constitutes phytoremediation, as soon as I got back to my laptop. 

Let’s start from the beginning. Let’s take hydrocarbon contamination. Wait, what are hydrocarbons? Hydrocarbons are a wide range of molecules composed by a variable number of carbon, oxygen, hydrogen and other atoms organized in a linear or circular manner. When these atoms are organized in rings, we call the molecules polycyclic aromatic hydrocarbons (PAH).  What is cool about these hydrocarbons, is that they are originally formed from organic matter in decomposition. Some of these molecules are caused by incomplete combustion of organic matter (PAH), and others result from changes in the organic matter physicochemical structure when it is buried way below ground at high pressure (oil, gas).

And why do I think this is cool? Let’s think again about one of the most important ecosystem services that biodiversity provides to us: organic matter recycling. A remarkably high number of living organisms contributes in one way or the other to the transformation of dead organic matter into accessible inorganic molecules, such as CO2, N2, O2, H2O, etc. From small arthropods that will break down fallen leaves in autumn, fungi that use these small shredded pieces of organic matter as a substrate to live in, to bacteria that munches on small molecules of this decomposing organic matter to close the cycle, returning nutrients in the form of inorganic molecules to the atmosphere, water basins or soil. 

Coming back to our hydrocarbons, their structure strongly resembles the physicochemical structure of the organic matter fungi and bacteria feed on. In fact, this resemblance is so important that many of the enzymes involved in the degradation of organic matter have a wide specificity. As a result, many bacteria and fungi have often been found degrading oil derived hydrocarbons.  How cool is that, right? 

The fact that microorganisms can degrade these complex hydrocarbons is so awesome because it means that we can rely on the power of the microbial enzymatic machinery to clean the collateral contamination derived from industrial, economic and social activities. The microbial enzymatic machinery will transform cytotoxic hydrocarbon molecules into inoffensive CO2 (regarding the effects of the accumulation of CO2 and CH4 in the atmosphere we can talk another day…). 

Can you see where I was heading with the superhero and villain metaphor? Well, maybe not yet. And that’s ok. Just keep reading! So, these holy molly superheroes of microbial degraders (now you know from where it came the superhero reference, right?) are everywhere. Especially in soils, there is a huge reservoir of microbial diversity that can tackle complex organic matter molecules, including oil derived hydrocarbons. But wait for it! Simultaneously, we have the holy grail mother of all transformations in soils: plants! and earthworms. Plants, as any other living being, are complex holobionts, and by that I mean each plant is not purely one organism, but it hosts thousands of millions of microbes, attached to its surface or thriving inside its tissues. In other words, a plant holobiont is more like a community of individuals of different species rather than a single organism (you are an holobiont as well, by the way, never alone). And guess what, there are potentially thousands of microbial degraders ready to tackle hydrocarbon contamination in the root system. BOOM! Do you see where I’m going? 

The relationships between the plant and some microorganisms of the root system is so strong that allow the plant to survive in a contaminated environment that would kill any other plant lacking these strong microbes in their microbiota. 

In the past few decades, we have been using these plants containing microbial degraders in their roots to decontaminate polluted soil, applying a revolutionary technique that we call phytoremediation. By nature, phytoremediation is an ecological and cheap decontamination technique that exploits the relationships occurring between the plant and the associated microbes to decontaminate soils. So, just like that, phytoremediation renders these soils safe for supporting other forms of complex organisms again.

Phytoremediation can be direct or indirect. The direct mechanisms correspond to the plant stimulation of microbial enzymatic activity in the root surface. The plant can do this by the exudation of some photosynthesized compounds that resemble the hydrocarbons structure. This stimulation occurs naturally and allows the microbial community to rapidly respond to contamination when the microbes are in a contaminated soil. 

The indirect mechanisms involve the stimulation of the root development by the microbes. Some of the microorganisms living in the rhizosphere can stimulate plant growth through either the production of molecules that mimic plant hormones or the consumption of certain plant hormones that limit plant growth. As a result, the plant develops a larger root system harboring more degraders, which in turn means the degraders can access further areas of soil, thus increasing the total amount of soil that can be decontaminated.
We know this system works, around 40 years of work have demonstrated the ability of different plant species and microbes to decontaminate a plethora of hydrocarbon compounds. 

Now the question is: how is the diversity component of the plant holobiont affect the outcome of the phytoremediation strategy? Does the diversity of the microbial community drive the success? If so, through which components of microbial diversity? Species richness? Functional redundancy? Complexity of holobiont interactions? Also, in contaminated soils many small invertebrates survive to high levels of contamination, in such a way they could still be influencing the microbial community or the plant root system. These organisms have also their own set of microbes in their digestive systems that could be potentially contributing to the degradation of the hydrocarbons… The question of the soil diversity affecting the plant holobiont in a context of decontamination can quickly escalate into a very complex problem.

You see? That’s why sometimes I just give a short, complex, annoying paragraph-like sentence to answer whenever someone asks for my PhD subject. I can get intensively engaged in a monologue, completely forget my manners and ask the question back! At least now, dear reader, if you got down here you learned quite a bit about phytoremediation, or the art of tackling soil diversity to decontaminate soils. 

Sara Garcia is doing her PhD with Pr. Etienne Yergeau at Institut National de la Recherche Scientifique – Armand Frappier Santé Biotechnologie Laval, and she is co-supervised by Dr. Armand Séguin at Natural Resources Canada – Forestry Center. Sara is intrigued by the ecology of the plant-soil interface and the interactions between soil microbes and fauna under hydrocarbon contamination.

Post date: November 22, 2019


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