Microbes Matter: Why bother with the small things?

By Tony Pattison, Department of Agriculture and Fisheries 

Soils are teaming with life, with up to five tonnes of soil organisms per hectare (e.g. bacteria, fungi, protozoa, nematodes, and many others). While some species are damaging to plants, causing diseases, many more are beneficial (See Fig 1). They suppress diseases and enhance nutrient availability, making significant contributions to agricultural production, at no cost to growers. 

The big question is how do we manage farms to maximise these benefits to ensure they continue to support plant production? Until recently, it was extremely difficult to study soil microbes and their communities. 

This is because many soil microbes look alike, are invisible to the naked eye, and tend to be difficult to grow in the laboratory. Advances in DNA-technology, however, make it possible to identify microorganisms, and their interactions, abundances, and functions. These approaches use the fact that each organism has a unique genetic code. 

The genetic code of bananas is made up of around 36,000 genes that act as blueprints to make banana plants what they are. However, bananas are not alone, they associate with tens of thousands of microbial species (‘the banana microbiome’) that all have additional genes to contribute. In fact, these microbial genes collectively exceed those of the plant by 10 times, meaning that bananas are associated with a much wider range of genetic functions than just their own genomes. This is like accessing information from the internet, compared with just getting information from the local library. 

Consequently, it is important to better understand the banana microbiome, as they can have greater potential in maintaining plant health than manipulating plant genes alone. 

To make the most of the banana microbiome we need to understand what the different organisms do, how they interact with plants and each other. 

Generalisation of functions of the microbiome (Fig 2) include. 

• Organic matter turnover 

• Nutrient transfer 

• Soil structure improvement 

• Disease transmission and suppression 

• Chemical pollutant degradation and 

• Greenhouse gas production 

It is when these organisms are no longer present and no longer functioning that we can really appreciate their value. For example, we have found that the fungus that causes Panama Disease was 2500-fold more successful in colonising sterilised (dead) soils, when compared with non-sterilised samples of the same soils (Fig 3). 

Soil sterilisation is an extreme example, comparing living and dead soil, but there are farm practices that can impair the microbiome, decrease its function, and reduce plant fitness. These practices can increase the impact by root pathogens like fungi, bacteria and nematodes. 

Furthermore, the loss of the microbiomes can make plants more susceptible to environmental stress, heat, cold and moisture. To better utilise the banana microbiome, we need to better understand the organisms that make up the microbiome, find out what they do, and how to control them. We also need to understand how growing bananas has changed the microbial makeup, then how to manipulate the organisms and make use of their genetic potential to maintain plant fitness (Fig 4). 

These issues have been investigated or are under investigation from the partnership between the University of Queensland team being led by Dr Paul Dennis and the Department of Agriculture and Fisheries team being led by myself (Dr Tony Pattison), with financial support from the Australian Centre for International Agricultural Research (ACIAR). 

In the next issue we will show how growing bananas has altered soil organisms.