A UCC team is studying the invisible world where billions of bacteria live, in the soil beneath our feet. Dick Ahlstrom reports
The soil under our feet teems with life, yet it is a living world beyond our ken. A paperclip's weight of soil can contain up to 10,000 different species of microbes with individuals counted in their billions.
A research team at University College Cork hopes to open up this mysterious world by learning more about bacterial species in the soil. More particularly the goal is to understand how human activity and climate change impact on these organisms.
The research is known collectively as "environmental genomics", says Dr Julian Marchesi, a lecturer in UCC's microbiology department.
The subject has come in for intensive study around the world since the advent of human genome sequencing given that the same technologies are used whether the DNA comes from a human or from a bacterial species in the soil.
"Genomics is the study of genes in the human genome. What genes do we have, and what do they do," says Marchesi. "With environmental genomics we look at how the environment impacts on bacteria. We take the technology used with humans and use it with bacteria in the soil."
The subject includes the study of any species, for example how fish respond to river pollution or insects to industrial discharges.
The Cork group, however, is specifically interested in soil bacteria. The real challenge is being able to cope with the invisible yet extensive life that exists in the soil.
"A gram of soil is as rich [in biodiversity terms] as the rainforest," says Marchesi. "At the basic level they are the foundation of life on earth."
How the bacteria respond to stressors is not simply of academic interest, he argues. There are crucial interactions between plants and bacteria in the soil, for example for fixing nitrogen or leaching required nutrients from the soil.Yet little is known about how overuse of fertiliser, for example, might affect essential bacteria.
"Pollution is another important one," says Marchesi. "What is the long-term impact on these communities, how do they react."
There is now an international effort to answer some of these questions. Late last month Marchesi organised and UCC hosted an international conference, Environmental Genomics: Future Microbiological Perspectives. The conference was sponsored by the Society for General Microbiology and included speakers from the UK, Spain, Germany and Ireland.
The techniques being employed by Marchesi would be familiar to any geneticist using the new technologies. It involves genomics, proteomics and the study of bacterial metabolites.
The tools used include PCR, DNA sequencers and data mining, using the extensive store of DNA sequences provided by international teams in the search for shared genes.
"Bioinformatics is very important in this work," says Marchesi.
The hope is that environmental genomics could play a significant part in reaching a better understanding of environmental problems and possible solutions.
"We need to understand how the bacteria respond," he says.
"There are many microbes there that we could exploit as well. There is the potential to use them as sensors for the environment," he believes. "We are trying to get a better understanding of what is happening in our environment."
Bacterial populations react quickly to stressors of all types and they could provide an early-warning system to help identify when something is going wrong, he says.
We are only just beginning however to unveil the secrets of this microbial world.