Harnessing the invisible and invaluable microbes that enhance our food, environment and health

By November 17th, 2022

What do our gut microbiome, soil, persistent chemicals and dung beetles have in common? That’s what our MOSH Future Science Platform is working to find out.

Our MOSH future science platform aims to create a species-specific designer microbiome for dung beetle eggs so they grow into healthy adults that can tolerate the Australian environment and work on clearing cattle grazing pastures.

We normally associate microbes with disease but in fact there are many that can improve the quality of our lives on this planet. What would we do without yeasts to make fermented foods, for example, or the bacteria that decay matter and fertilise the soil?

Microbes don’t operate alone. They form communities, called microbiomes, where they work together as a system. Like microbes, microbiomes are invisible to the naked eye and are essential to the function of all living things. You may have heard of the human gut microbiome – the community of microbes we all cart around inside us, and that science is learning is vital to our overall health and well-being.

At CSIRO, we’ve established the ‘microbiomes for one systems health’ (MOSH) Future Science Platform to research microbiomes in various ecosystems and to develop new understanding of how these microbiomes might be connected.

The goal of this frontier science effort is to be able to predict the effects of disruptions – beneficial or detrimental – on microbiomes, to directly manipulate microbiomes for targeted interventions and hopefully to harness their benefits for our health, our food and our environment.

Some of the microbiomes we’re researching include:

Dung beetle egg microbiome

The average cow drops between 10 and 12 dung pats every day. With a national herd the size of Australia’s, that’s a huge amount of dung produced annually. By burying cow dung, dung beetles help improve soil, reduce the spread of flies, pest and disease, and reduce the amount of nutrients washing into waterways. However, it’s imported dung beetles that are currently used to clean up cow dung in Australia, a job native dung beetles don’t want to do. Imported dung beetle eggs are sterilised during the quarantine process, which removes their natural microbiome and results in poor dung beetle establishment and survival.

MOSH aims to restore the microbiome of the sterilised eggs of imported dung beetles, post-quarantine. By understanding what microbes play an important role for the host beetle, we can create a species-specific designer microbiome to inoculate the eggs. The added microbiome will allow the dung beetle to develop into healthy, reproducing adult beetles that are able to tolerate the Australian environment, so that they can get to work clearing cattle grazing pastures.

Designer microbiomes for bioremediation

We’ve been working with industry partners to clean up contaminated sites through the use of microbes, a process known as bioremediation. Despite increasing our understanding of the role microbes play in contaminant removal, a number of challenges have previously limited the success of bioremediation strategies. Most notably, microbes failing to survive in the environment long-term and their performance varying for reasons not yet known.

This is particularly the case for per- and polyfluoroalkyl substances (PFAS), often referred to as ‘forever’ chemicals for their persistence in the environment. Furthermore, these chemicals are ubiquitous, bioaccumulate and have been shown to have adverse health effects.

MOSH aims to identify individual microbes in these contaminated environments involved in the degradation process of persistent chemicals. We aim to then culture these key microbes and develop designer microbiomes that give them everything they need to do their job. This should ensure they can not only survive in contaminated environments but also clean up the mess.

Plant health microbiomes

Plants are host to a diverse and interconnected community of microbes that provide essential services, such as sourcing and mobilising nutrients, enhancing plant growth, deterring disease and bolstering the plant’s tolerance to environmental stresses. Despite this, what impacts the plant host-microbiome relationship in agricultural environments, is still poorly understood.

By understanding how food crops of global importance, such as wheat, interact with their microbiome, we hope to enhance the health of food crops using targeted interventions to the microbiome. This will help develop sustainable production systems by preventing crop losses from disease and environmental stresses, including drought and changing climate, and better meet growing demand for global food supplies.

Nature’s fungicide

Disease suppressive soils are those that, because of the soil microbiome, limit infection from pathogens in the soil to the root, resulting in little or no disease in the plant. One such pathogen, Rhizoctonia solani, is known for causing root rot and bare patch disease in a range of cereal crops in non-suppressive soils. It has been estimated to cause $77 million damage to wheat and barley crops each year. Fortunately, disease suppression of this pathogen has been documented in defined areas in Australia, giving hope that native microbiomes can fight off this pathogen.

MOSH researchers will use multi-omic techniques to understand the makeup of these special soil microbiomes and how they function to supress disease. We can then develop targeted interventions to enhance the biological suppression of pathogens such as R solani. This research has the potential to develop management options of agricultural land that promote beneficial soil microbiomes that reduce the use of fungicides and herbicides, and the impacts of disease on the production of food crops.

The fungal species Emericella rugulosa growing on cotton crop residues in soil at Narrabri, NSW. We need to get up close and personal to understand microbiomes better. Each of these fungal ascospores is around 4 micrometres across, whereas the average human hair is about 80 micrometres.

Food chain microbiomes

Foodborne illness costs Australia $2.44 billion each year, mainly through loss of productivity. Furthermore, food waste is a major issue with 7.6 million tonnes of food wasted across the supply and consumption chain, accounting for a loss of $36.6 billion each year. A large proportion of food waste is due to spoilage of consumable plants.

To help combat this problem, we’re investigating the food chain microbiome, specifically how post-harvest conditions and washing treatments impact microbial communities in baby spinach.

Other microbiomes

MOSH is also researching other microbiomes that are part of the continuum from the environment through to humans:

  • Soil-water waste microbiomes to control the transfer of antibiotic resistant genes from the environment to human-animal gut
  • Enhancing the gut microbiome of black soldier flies to improve their health and ability to degrade biosolids from waste-water treatment
  • Animal health microbiomes, building on our world-first work with industry partners where we developed a tool, ImmuneDEX, that allows Angus beef producers to improve the health of their herds based on their immune system. A better understanding of how the host immune response influences the microbiome will lead to interventions that result healthier cows requiring less antibiotics, also reducing antibiotics in our food production chains

Human gut-microbiomes, where MOSH is developing approaches to improve the gut microbiome function for better human health.

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