Why is the soil microbiome important for sustainable agriculture?

The microorganisms present in the soil can have a considerable effect on the health of crop plants. Different types (species or strains) of bacteria and fungi can cause plant diseases or have beneficial effects on plants such as an increased yield. Understanding how to change the structure of the microbiome to promote beneficial microbes and reduce detrimental ones could be key to increasing crop production in a sustainable way. In the final and third part of her blog series, Research Assistant for Genomics and Molecular Diagnostics, Dr Victoria Woolley explains more.

How does the soil microbiome affect crops?

It’s been known for decades that microorganisms in the soil can be beneficial or detrimental for crop health. Some of the first groups of microbes that were identified as being beneficial to plant growth were the mycorrhizal fungi and rhizobial bacteria, which are both associated with the roots of certain plants.

Rhizobial bacteria trigger the formation of root nodules of legume plants (e.g. pea, bean, clover), which they are then contained in. These bacteria receive nutrients from the plant and produce nitrogen in a form that can be used by the plant for growth and grain production. Mycorrhizal fungi also form associations with plants roots, they provide the host plant with increased nutrient uptake from the soil and improved abiotic stress tolerance, whilst the fungi receive carbon from the host plant.

Disease-causing bacteria or fungi can infect plants via the soil and can result in large reductions in crop yield. These microorganisms may be able to survive in the soil for years, waiting for a suitable host plant to infect which can make their management difficult. However, other microorganisms in the soil can help combat these pathogens by outcompeting them, attacking them and priming the host’s immune system. For example, species of the fungus Trichoderma are found in forest or agricultural soils (CHAP NRC isolates). They can control disease-causing fungi by competing for space and nutrients, parasitising the fungi and increasing resistance of the host plant to the pathogenic fungi.

It’s not only individual microorganisms that are important to crop health, but the function of communities as a whole. Understanding the core microbiome of a healthy plant is a developing area of research and could provide insight into novel treatments or farming practices that promote a complete healthy microbiome.

Can you modify the soil microbiome?

Yes you can! Recently modification of the microbiome has focused on inoculation with a single microbial species, but there is increasing interest in promoting a healthy microbiome through improved soil health and developing synthetic communities (SynComs) of microorganisms. This can increase crop’s tolerance to abiotic stress (extreme temperatures, droughts), improve crop’s nutrition to increased growth and increased resistance to disease. This has the potential to reduce the needs for chemical inputs such as pesticides or fertilisers and support sustainable agriculture.

However, there are a number of challenges around altering the microbiome in agriculture. Firstly, it can be difficult to apply microorganisms to crops as they are susceptible to stress including temperature, humidity and UV light. Furthermore, they may behave differently in fields to laboratory/field trials due to different environments and interactions with indigenous microorganisms. There are also difficulties in identifying organisms in the soil microbiome and culturing them to allow their use in agriculture.

Farming practices can be used to promote healthy soils and a healthy microbiome. These include regenerative agricultural practices such as direct drilling and intercropping (Regenerative agriculture: a vision for the future) that promote a more diverse soil microbial community. It also includes reducing the application of potential harmful inputs such as pesticides and fertilisers which can negatively impact beneficial microorganisms. For example, mycorrhizal fungi are negatively affected by high levels of inorganic fertiliser and the application of animal manures or vegetable mulch is better for them.

What does the future look like for microbiome research?

In order to better understand and develop ways to use the soil microbiome in sustainable agriculture we will need to use a more holistic approach for research and development. This will involve using a multidisciplinary approach to build a complete understanding of the microbiome and will require steps such as:

  • Storing and maintaining the viability and functionality of microorganisms (cryobanking).
  • More accurate and rapid identification methods (link to article 1 ‘What is the soil microbiome and how do you measure it?’).
  • Sampling and detection of microorganisms in field (link to article 2 ‘Three ways ‘Omic’ technologies are lifting the lid on the soil microbiome’). This may involve the application of robotics and portable molecular diagnostics tools (e.g. Nanopore minION).
  • Data mining, linking microbiome composition to healthy crop systems.
  • Development of prediction tools and decision-making tools.
  • Investigating the impact of agricultural practices on soil health and microbiome composition.

CHAP can help achieve this by acting as a nexus, bringing together researchers and industry from different disciplines to help meet farming needs. CHAP’s expert network can help you identify how the microbiome research can contribute to achieve your goals and strengthen developments towards sustainable agriculture.