BactoTrapS for Bioremediation

Bioremediation is the process of using microorganisms to clean up contaminated soil. Certain bacteria feed on waste products, including pollutants released into the environment by humans. Some bacteria can naturally break down pollutants such as hydrocarbons, which are found in petroleum products or are generated during the combustion of fossil fuels.

However, as these pollutants form a complex mixture of molecules, a single bacterial species is often unable to tackle the entire pollution problem alone. A group of different bacteria, known as a consortium, is much more effective at eliminating all of the pollution. However, even though these bacteria are present in the soil, they are often found in very low concentrations.

The MIBIREM Project: Boosting Nature’s Cleanup Crew

 

The MIBIREM project therefore aims to isolate bacterial consortia capable of degrading various organic contaminants, study them, and then reintroduce them in large numbers into the soil – a process known as bioaugmentation. But how can such consortia be obtained? Traditional microbiology methods can be employed to enrich and cultivate bacteria in liquid media. However, the problem is that not all soil bacteria thrive in these highly selective laboratory conditions.

A “tea bag” for bacteria that helps clean up polluted soils

So, we designed a system for capturing soil bacteria. It is easy to imagine how to capture an animal. What would you use? A trap, such as a cage. Well, we have designed a cage for bacterial that we have named BactoTrapS. It is like a tea bag: it’s a bag filled with an inert mineral on which we have deposited the pollutant we want to degrade.

The bag is highly porous, allowing only microorganisms to pass through. When the bag is buried in the soil, if any bacteria like the pollutant contained in the bag, they will be attracted by a phenomenon called chemotaxis. The bacteria will move into the bag, eat the pollutant and, as they are comfortable there, they will even multiply.

Meet BactoTrapS: A Tiny Cage for Microbes

We tested these BactoTrapS by contaminating them with different types of hydrocarbon. Our trap worked! After leaving the bags in the soil for five weeks, we captured some very unusual bacteria. Most of them were capable of breaking down hydrocarbons. To demonstrate this, we divided the substrate contained in the bag into two parts. From the first half, we extracted the genomic DNA of the captured microorganisms and sequenced it to identify all the bacteria captured. We demonstrated that the bacteria captured in the bag containing hydrocarbons differed significantly from those captured in a control bag containing only the inert mineral substrate.

On the second half of the substrate, we removed the bacteria and cultured them on solid media in the laboratory (in Petri dishes). The advantage of this second approach is that it enables us to test the biodegradation capacity of each bacterium individually. These bacteria can then be used in the MIBIREM project for the bioaugmentation of hydrocarbon-contaminated soils.

Going Beyond Hydrocarbons

This work, described in detail, was the subject of a scientific publication in the Journal of Hazardous Materials published at the end of February 2025 by the MIBIREM project partners CNRS-French National Centre for Scientific Research. These BactoTrapS proved highly effective at trapping bacteria. We now also have used them to capture bacteria that were resistant to a very recalcitrant organochlorine pesticide called lindane.

 

Author:

Aurélie Cébron,

Director of Research,

CNRS-French National Centre for Scientific Research