PLANT science – helping uncover mysteries of soil bacteria

By Margarita Kalamara, University of Dundee

On Sunday the 25th of June we had a wonderful day at the Tayport community gardens at a citizen science event! The workshop was a collaboration between P.L.A.N.T. and our group from the Division of Molecular Microbiology, University of Dundee, where we explored the hidden world of microbes in soil and collected bacteria to use in our research. Around 20 different family groups came to the event to help us with our work.

Bacteria are microscopic creatures that live in pretty much all habitats- from bathtubs to hot springs and on and in our bodies. As humans we tend to associate bacteria with disease and dirt, which is to an extent true. However, while some bacteria do make us ill there are also multiple ways in which they are hugely beneficial to us and our world. For example, bacteria can be used for the production of biofuels and make electrical energy, they can help us make specific types of food such as yoghurt and they play a vital role in our ecosystem by being the final link in our food chain.

95% of the food that we consume comes from soil directly or indirectly. Soil is home to a huge diversity of life – a single gram can contain up to 10,000 species of bacteria! These tiny organisms decompose organic matter (including fallen leaves and dead animals) and recycle nutrients that are trapped within it. Once the nutrients are released into the soil they can be taken up by plants to fuel their growth and contribute to the food chain. The soil ecosystem is very lively and we still don’t know a huge deal about it. We do however know that some bacteria are very important in keeping our plants happy and healthy; by attaching to plant roots bacteria help our crops take up nutrients and protect them from disease. This is because some soil bacteria produce antibiotics that kill the bad guys (“pathogens” as we call them) in the surrounding area. The helpful bacteria are sometimes called biocontrol agents and can be useful in agriculture as a sustainable alternative to chemical pesticides and fertilisers.

As researchers in Microbiology, we are fascinated by how “simple” single-celled bacteria build complicated communities which we call biofilms. Bacterial biofilms are covered by a slime (also known as “matrix”) which provides the members of the community with protection from harmful things in their surrounding area (such as physical forces or antibiotics). This makes bacteria in biofilms more resistant to environmental insults. As bacteria can be both good and bad for us, biofilm formation can be very harmful (e.g. when biofilms of pathogens form in our bodies) or very useful to us humans (e.g. when biofilms of biocontrol agents form on roots of crops). By researching and understanding how biofilms form we hope to find ways to promote or prevent formation of biofilms according to our needs.

The star of the show in our lab is a plant-helper bacterium called Bacillus subtilis. B. subtilis is sold as a biofertiliser and biocontrol agent as it helps plants take up phosphorus and produces many different types of antibiotics that can kill plant pathogens. Using a specific isolate which is widely used in research by labs worldwide, we have made great progress in understanding the mechanisms by which this organism forms biofilms. What we don’t yet know is how widespread these mechanisms are amongst “natural” environmental isolates of this species. To what extent do these mechanism apply to B. subtilis (and its close relatives) found, say, in people’s garden soils?

Through our citizen science event we asked members of the public to help us answer these questions by bringing in some soil from their garden and doing the first part of the experiment with us. We took the soil, processed it and placed it on bacterial growth media. Below are some of the growth media plates that contain a diverse range of bacteria from different soil samples, mainly from Tayport.

The first event was a success! We collected 30 garden soil samples and isolated 90 different types of B. subtilis and closely related species. We are now in the process of looking at biofilms of the different isolates and characterising them.

Our second citizen science workshop is on the 23rd of July at from 2-4 pm at the Tayport Community Garden. Come along with 2 tablespoons of soil from your garden or compost to do some experiments with us, find out what’s in it and help us further our research!

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