Putting bacteria to work

By Dr Peter H. Janssen, University of Melbourne

Soil microbiologists at the University of Melbourne are unlocking the secrets of soil bacteria.

Using new research techniques, they are opening the way for investigating the vast potential of soil bacteria for suppressing disease, enhancing soil structure, promoting plant growth, or tapping nutrients for crops.

Conventional techniques for growing soil bacteria have previously revealed only the “tip of the iceberg” because they captured and cultivated only about one percent of soil bacteria.

Each gram of soil, about a teaspoon full, has about one billion bacteria in it.

Each bacterium is a separate, single-celled living organism, involved in nutrient cycling and contributing to soil structure.

Farmers would like to get these bacteria working for them. However, to harness soil bacteria for a more productive or sustainable agriculture, we need to know what these bacteria do in the soil. Even after 100 years of soil microbiology, we do not know.

The main problem has been to find ways of studying them. Microbiologists study soil bacteria by first dispersing the bacteria in a small sample of soil onto the surface of a nutrient containing gel in a Petri dish.

The bacteria themselves cannot be seen on the surface. Each is less than one one-thousandth of a millimetre long.

However, the cells can now use the nutrients in the gel to multiply. After a while, each cell has given rise to so many progeny that they form a visible clump a few millimetres across, made up of millions of identical microscopic cells.

By taking a part of a colony, and spreading it onto new gel surfaces, it is possible to keep the bacteria alive in the laboratory and study their properties. This is how microbiologists came to learn so much about soil bacteria during the 20th century.

Each of the colonies on the gel surface arises from one cell. What is surprising is that only about one cell in every one hundred in a soil sample is able to grow to form a colony on the gel surface, while the other 99 do not. We do not understand them well enough to provide the conditions they require to multiply to form colonies.

If they do not form colonies, we cannot study them. Since 1918, when this problem was first pointed out, soil microbiologists have always had a nagging doubt.

How representative of all soil bacteria is the one percent that forms colonies?

In the 1990s, microbiologists started using one of the genes found in all bacteria as a kind of “identification barcode”.

The order in which the four nucleotides (A, G, T, and C) are used in the gene is essentially unique to each species. The order of the nucleotides in this “barcode” gene, called the 16S rRNA gene, can be analysed directly from the soil.

What microbiologists found was that 99 per cent of the 16S rRNA genes in the soil are new to science. This means that 99 percent of bacteria in soil are new to science too, about 4000 different species in a gram of soil. There are whole groups of soil bacteria that have never been studied in the laboratory.

We do not know anything about their properties. The early soil microbiologists were right to have their doubts. The bacteria that form colonies on nutrient-containing gels are not representative of soil bacteria. They are only a very small minority.

In the past few years, the team in the Janssen laboratory at the University of Melbourne have discovered how to grow many of these so-called “unculturable” soil bacteria. They are now able to cultivate many of the groups of bacteria that have eluded previous generations of soil microbiologists.

This means that we finally have the opportunity to discover what the remaining 99 percent of bacteria do in the soil, and how they may be utilised for the benefit of farmers and the environment.

For more information:
Dr Peter H. Janssen, Department of Microbiology and Immunology, University of Melbourne
pjanssen@unimelb.edu.au