Putting food under the microscope

Could microbes hold the key to sustainable agriculture?
25 January 2019

Food market

Fresh fruit and vegetables at a food market


You might think that microorganisms - aka microbes - contaminate food, cause disease and are generally something to be avoided. But we shouldn’t be afraid of the microbes in our food...

“Current dietary trends, combined with projected population growth to about 10 billion by 2050, will exacerbate risks to people and planet. The effects of food production on greenhouse-gas emissions, nitrogen and phosphorus pollution, biodiversity loss, and water and land use will reduce the stability of the Earth system.” - The Lancet [1].

So the world soon needs to feed 10 billion and do it without destroying the planet in the process. Consequently, scientists are turning to some of the smallest life forms for help. Our world is teeming with microscopic life, which come in the form of bacteria, fungi, algae and archaea. These microorganisms have a huge range of different metabolic lifestyles. Decomposers recycle dead matter; photosynthetic microorganisms are literally solar powered, and others fuel their growth using hydrogen, sulphur or methane. It is because of this biochemical diversity that microorganisms are so essential to the food chain. And as our understanding of what microorganisms are capable of improves, researchers are discovering new processes for food production and even rediscovering the potential of lost traditional practices replaced previously by technological progress.

Starting with soil, the dirt beneath our feet isn’t just a source of water and minerals; it’s a whole ecosystem teeming with microscopic life. Plant roots grow down into the soil, reaching out to form beneficial associations with microorganisms. These interactions involve chemical exchanges that enable plants to acquire nutrients like nitrogen and phosphorous.

But in agriculture, rather than relying on these natural associations with microorganisms, fertilisers are used to enrich the soil with nutrients and enhance crop yields. However, these fertilisers wash into our rivers, streams, oceans and seas, and can cause major problems to biodiversity. Also, as highlighted in the Clean Air Strategy 2019 [2] recently published by the UK Department for Environment, Food & Rural Affairs (DEFRA), fertiliser use greatly contributes to greenhouse gas emissions. “When you spray the soils with these nitrogenous fertilisers some of it is converted to gaseous forms of nitrogen, called nitrous oxide, and they're incredibly potent greenhouse gases. They’re about 35 times more potent as a greenhouse gas than carbon dioxide,” explains Giles Oldroyd from Cambridge University’s Sainsbury Laboratory.

“There's a huge potential here to bring the power of soil microorganisms into agriculture for the acquisition of nitrogen and phosphorus”. One group of microorganisms called nitrogen-fixing bacteria, are able to take nitrogen from the air and turn it into a form that works as a fertiliser. But only some plants, called legumes, like peas and beans, have evolved the capability to team up with these bacteria to allow them to benefit from this process. Oldroyd leads a team of scientists who have identified specific genes that allow legumes to form these associations and are now trying to move these genes into plants like barley that currently can’t [3].

Although this research is still in the early stages, some people might be concerned about the use of such genetically engineered crops. For example, if the seeds escape from the field they are being grown in, they could encroach on natural habitats and might out-compete native species. “We'd have to consider the safety implications for both the environment and for human health,” says Oldroyd. “But I think that right now the potential of this technology, particularly the potential of the technology to reduce agricultural pollution, is so great that we really have to crack on and do it. Acknowledging that those risks exist and doing what we can to mitigate those risks.”

Methane burps and the charms of fermentation

The DEFRA report states that “agriculture also accounts for around 51% of methane emissions.” Cow burps are a major source of methane, which is produced in their stomachs by a group of microorganisms called archaea. Methane production is not just harmful as a greenhouse gas, but it also represents a loss of energy to the cow. “There's a lot of research ongoing, looking at different ways of reducing methane,” explains Chris Creevey from the Institute for Global Food Security at Queen’s University Belfast. “These are taking different forms. Some additives into feed such as the algae is a very interesting potential for reducing methane. Other ways which may work and which are being investigated are looking at breeding animals, because you may be able to breed them to produce less methane; or maybe even you can inoculate them and give them a vaccine to produce their own antibodies to specifically reduce the archaea in the rumen.” [4]

Beyond just methane emissions, many studies over the last year have highlighted the extensive environmental impact of livestock farming. There is a growing consensus that a plant-based diet is needed to sustainably feed a growing population [1,5]. Could turning to our microbe friends help us unlock the full flavour potential of plants and entice us into eating a plant-based diet?

We all have experience of microorganisms growing on our food and causing it to rot. Gooey black spots develop when we leave our food lying around for too long. But by keeping food in the correct conditions you can selectively nurture microorganisms that perform fermentation reactions. For example, by adding a bit of salt to fresh cabbage and leaving it in an airtight container, overtime the microorganisms naturally found on the cabbage leaves will do their biochemical thing and give us sauerkraut. Fermentation broadly refers to the processes by which the enzyme activity of microorganisms causes food to breakdown, which produces things like acid, gas and alcohol. This process can create complex flavours and also help us preserve food.

By selecting for beneficial bacteria over harmful pathogens, fermentation extends the shelf-life of food without the need to cook it or freeze it. Therefore, fermentation could be a low energy-intensive solution to minimising food waste.

You could say that the holy-grail of plant-based foods is a "meaty" meat-free burger. Several companies are developing alternative protein sources to meat and these often rely on fermentation processes. One example already widely used is derived from fungi and is called mycoprotein [6]. The company Impossible Burger have developed a technique based on fermentation to produce an iron containing molecule called heme that is believed to be the secret to why meat tastes so uniquely meaty [7]. The world-renowned restaurant in Copenhagen, NOMA, also has fermentation at its centre. NOMA runs a fermentation lab that takes inspiration from this ancient technique of breaking down food using microorganisms to discover new flavours for their innovative menu.

Embracing biodiversity and overcoming our obsession with sterility

As the fermentation process demonstrates, our obsession with keeping food in a sterile environment is not always sensible. Cheese is the perfect example of this. In their book Reinventing the Wheel: Milk, Microbes and the Fight for Reel Cheese [8], Bronwen and Francis Percival write, “Safety through sterility is an approach that is so comfortingly obvious that we have taken it for granted for more than a century, both in our food production and in our daily lives.” However, when it comes to cheese, microorganisms are fundamentally important for creating the rich diversity of textures, smells and flavours the we love.

Mass-produced cheese typically relies on starter cultures used to add a select group of microbes to pasteurised milk. But this has not always been the case. “If you look back about 120 years, nobody was adding microbes to the milk that they were using to make cheese. Milk is sterile when it leaves the udder of a healthy animal but then it has many opportunities to be inoculated with naturally occurring microbes from the environment and that could be from the udder, from the skin of the teat,” explains Bronwen Percival. Each farm will have its own microbial footprint that can impart specific flavours to the cheese as it matures. By embracing biodiversity at every stage of the cheesemaking process, from the meadows cows graze on to the microbial community in raw milk, farmhouse cheesemakers have the capability to make cheeses with tastes that are truly unique to their farm. In this way they can improve their chances of competing against the growing pressures of consolidation and efficiency in the mass production of cheese, while exciting our taste buds and reconnecting our experience of food with the land it comes from.

With technological advances in microscopy, genetics and DNA sequencing, our understanding of the significant role microorganisms play in agriculture is growing fast. Perhaps we need to look no further than the soil beneath our feet or the cheese on our plates to find inspiration and work with the mini biochemists that are all around us to sustainably feed our growing global population.


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