Under pressure: how do microbes grow in compacted soil?

Posted on September 2, 2014   by Jon Fuhrmann

This week, the Society for General Microbiology is hosting its first ever Focused Meeting, a mini-conference specialising on a specific topic within microbiology. This incarnation of the event is themed Emerging Challenges and Opportunities in Soil Microbiology and is taking place at the University of Loughborough. Jon Fuhrmann spoke to Archana Juyal, a PhD student from Abertay University in Dundee and a speaker at the event, about her research.

U.S. Department of Agriculture, Public Domain

Archana is interested in how the structure of soil – including factors such as its density, stability and porosity – controls the distribution and functioning of the bacteria that live in it. She notes that microbes play a crucial role in this ecosystem, regulating over 80% of all chemical reactions taking place in soil. These reactions break down complex chemical compounds, producing essential nutrients for plants and soil-dwelling animals.

Even relatively small changes in soil structure can have an important impact on soil microbial communities. For example, bacteria introduced into farmland soil to enhance crop growth may require certain conditions in order to function. This is because soil, far from being a continuous solid, consists of a multitude of tiny particles called aggregates. These aggregates are separated by gaps, known as pores, which allow nutrients, water and other essential chemicals to be distributed within the soil so that they are available for microbes, plants and animals to use.

One important factor that can affect soil structure is the use of agricultural machinery. As heavy objects such as tractors move over the soil, they compact it, increasing its ‘bulk density’ and destroying its pores. This can hamper the distribution of gases and chemicals and the flow of water through soil, which has been shown in several studies to have a negative impact on plant. But what about the growth of soil microbes?

This is where Archana’s research comes in. Over several days, she studied soil samples packed at different bulk densities to see how compaction affects the growth and spread of bacterial communities. To render the microbes visible, Archana used a method called Fluorescence In-Situ Hybridisation or FISH, which allowed her to quantify the number of bacteria in the samples without destroying them. A luminescent dye that binds to certain chemicals found within bacteria is added to the sample, illuminating the microbes and making them easily countable.

However, the organic compounds found within soil naturally fluoresce, so Archana used a specialised version of FISH called Catalyzed Reporter Deposition FISH, or CARD-FISH, to distinguish the bacteria from the surrounding soil.

The number of bacteria present in the soil was shown to be smaller with each increase in bulk density. More compressed soils also compromised the ability of the microbes to spread through the substrate, suggesting the destruction of soil pores restricts the movement of essential nutrients and chemicals, as well as that of the bacteria themselves.

The implications of Archana Juyal’s research for agriculture are potentially far-reaching. It will be interesting to see how machinery will be refined to minimise soil disturbance and allow beneficial microbes to flourish.

Talks on topics from across the field of soil microbiology are on offer at our First Focused Meeting. There’s still plenty of time to sign up for the next one, which will be on Modelling Microbial Infection.

Image: U.S. Department of Agriculture on Flickr under CC BY 2.0