Andrew Free: unsung heroes, using microorganisms to clear pollutants

Bioaugmentation is the process of manipulating a microbial community, specifically adding beneficial microorganisms to an environment, to enhance a biological process. There is potential to use this technique to improve a range of microbial processes, including bioremediation, waste treatment and GI tract health.

Anywhere where you have a complex community of organisms and you want to either add a new activity in it or modulate existing activities, adding new organisms is a potential way of doing that.

Problems with bioaugmentation

The microbes in complex communities are already very tightly knit, and there isn’t much of an ecological niche in which a new and different organism could survive. New, introduced organisms are usually outcompeted and quickly die out.

 These are natural, complex ecological systems, and they tend to be quite stable, or they tend to respond in fairly unpredictable ways to most changes in conditions.

Moreover, the lab is very different from real-world, complex microbial systems. You may have microorganisms carrying out a process perfectly in the lab but then find that this is not replicable in real environments.

Biostimulation

Biostimulation is where microorganisms already existing in an environment are stimulated to carry out a specific function by adding certain nutrients or altering conditions like temperature or pH. Biostimulation is typically more successful than bioaugmentation, as it does not attempt to alter the composition of the microbial community. 

There's so much scope in microbiology because there's that huge diversity of organisms out there. But understanding them and finding ways to control them is the problem.

One project Dr Free has been working on investigates bioaugmentation and biostimulation techniques to enhance the breakdown of hydrocarbon pollutants by soil microbes. This is known as bioremediation: using naturally occurring or deliberately introduced microorganisms to break down environmental pollutants. 

Hydrocarbon pollution is a significant environmental concern. Hydrocarbons (compounds consisting of hydrogen and carbon) are very toxic even at low levels. Examples include coal, gasoline and diesel fuel, hydraulic fluids and tar. Accidental spills and leaks in the extraction, production and transportation of these substances, improper waste disposal, runoff from urban areas, and more, can lead to these toxic compounds entering the environment. 

Once released, they’re almost impossible to remove. If they enter water sources, that water can be permanently polluted. This has severe impacts on both biodiversity and the livelihoods and health of people who live in surrounding areas. 

Current methods to clean up oil spills in water involve burning the oil in situ, skimming oil off the surface, or, in serious cases, using chemical dispersants to break up the oil. Methods to clean oil spills in soil involve simply removing all the soil from that area. These techniques are far from ideal and can cause further harm to the biodiversity of the area. It is therefore crucial to find better ways to clear these pollutants in situ.

Some rare species of microorganisms can degrade hydrocarbons

Hydrocarbons do naturally exist in many parts of the environment, such as from natural oil seeps. These are areas where crude oil and natural gas enter the ocean through factures and sediments, releasing hydrocarbons into the water. Many organisms have therefore evolved to take advantage of this, finding a niche in degrading these compounds. 

Assil, Esegbue, Mašek, Gutierrez and Free, scientists at Heriot-Watt University and the University of Edinburgh, investigated whether adding biochar affected microbial community composition and hydrocarbon degradation in soil contaminated with diesel oil. They used three different types of biochar, one made from softwood pellets at 550ºC, one from softwood pellets at 700ºC and one from rice husks at 700ºC.

The aim of the experiment was to find out whether 

• Biochar could act as a biostimulant and increase the ability of native bacteria to degrade hydrocarbons in the oil.
• Biochar could act as a microbial carrier to potentially use it to deliver these microbes to contaminated soil.

The full paper can be found here.

What they found

In the study they used sequencing methods to identify the microorganisms present. They found that diesel rapidly alters the composition of the microbial community, causing an immediate, drastic reduction in biodiversity. Species that are rare and undetectable in uncontaminated soil then dominate the community in diesel-contaminated soil. Many of these were found to degrade hydrocarbons.

Biochar was shown to help mitigate the drop in biodiversity, reducing the extremity of the loss. Over time it was also shown to alter the community composition and this varied depending on what type of biochar was used. Surprisingly, complete degradation of a specific type of hydrocarbons, known as n-alkanes, was prevented in the presence of biochar. The investigators postulated that this may due to the biochar absorbing some of the hydrocarbons onto its surface.

The investigators were also able to concentrate specific hydrocarbon-degrading bacteria on the surface of biochar particles. This is known as enriching the microorganisms on biochar.

The enriched soil bacteria (in the presence of SWP 700˚C biochar) were then isolated and shown to persist when added to soil in a bioaugmentation experiment. Two pure cultures have now been isolated from the enrichment: the A. calcoaceticus, isolated by Zac Bloxha, and a Pseudomonas chlororaphis strain isolated by Jimena Olabarría García. These two will be the focus of defined bioaugmentation experiments going forward.

Enriching microbes known to degrade pollutants like oil onto biochar particles is incredibly important, as it means biochar now has the potential to act a microbial carrier. It could be used to successfully introduce these microbes into polluted environments. Biochar provides a solution to many of the setbacks of current bioaugmentation techniques and means that severe pollutants like oil could be cleared in situ, not only in soil, but potentially in water too.