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Healthy soil is important, but what does it look like?

Without healthy soils, we’d have precious little food to eat. But this fundamental resource is being eroded by climate change and overuse of agrichemicals. Under severe threat are the communities of microbes which live in and around crops, helping them to thrive, yet we still know precious little about what our treatment of soils is doing to those microorganisms.

October 21, 2020

Without healthy soils, we’d have precious little food to eat. But this fundamental resource is being eroded by climate change and overuse of agrichemicals. Under severe threat are the communities of microbes which live in and around crops, helping them to thrive, yet we still know precious little about what our treatment of soils is doing to those microorganisms.

As part of our series on improving food security, we spoke to GROW Colombia’s Dr Nasmille Larke-Mejía, who is using metagenomics to find out what makes soil healthy and how this can drive sustainable agriculture.

Image: This article forms part of our series on Food Security, leading up to World Food Day on October 16.

Why healthy soil is important

“Everything comes from the soil and ends up in the soil, if you think about it,” says Dr Larke-Mejía of the De Vega Group at EI.

For Larke-Mejía soil health has been a lifelong passion. Growing up in the north of Colombia, where her father worked in a local mine, every day at around 1pm she would feel the earth tremble under her feet as explosions ripped through the ground. “I wasn’t a biologist then, but as a girl I thought - that’s horrible, they’re destroying the soil.”

Image: For Dr Larke-Mejía soil health has been a lifelong passion.

Image: For Larke-Mejía soil health has been a lifelong passion.

Years later, while studying microbiology at university, she would find herself learning about the process of soil reconstruction and exploring microbial life at that same mine.

“Engineers at the site explained their efforts to restore the landscape and told me that, despite their efforts, after a few years of having carefully removed the organic layer of soil and storing it away - affected by rain, the sun and not giving it what it needed - the soil slowly turns sterile,” she reminisces. Not entirely sterile, it turned out.

“They said the only thing they added to the mines was the explosive. That explosive is a combination of two things: ammonium nitrate, otherwise known as a fertilizer, and fuel oil,” she tells us of the nugget of information which inspired a Master’s project to see whether something might actually be growing in the desolate minescape. “I thought: that could be a source of nutrients.”

“I actually found out that they were growing like a probiotic,” she explains of her surprising discovery. “The place they were making the explosive was like a cultivation ground. As they were making the explosive, they were growing the bacteria right there without knowing it. So, when they put the explosive in the mines, they were feeding the bacteria to the mines too.”

As exciting a discovery as that was, for Larke-Mejía it is that sadness of imagining a barren, sterile landscape that has stayed with her, and fuels her passion for her research here at the Earlham Institute.

“They would talk about sterile soil, and I thought that would be the worst thing,” she says, wistfully. “Going back to a fertile soil is very, very difficult. After it’s ruined, regenerating its microbiota would take years and years. You’ll spend a lot of money trying to recover it, but it will never be the same.

“I go back to that first inspiration, in my work today, on how I got interested in soils.”

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Everything comes from the soil and ends up in the soil, if you think about it

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The Colombian Mine where Dr Larke-Mejía conducted her research into soil health.

What goes in gets eaten

As well as working on explosives for her Masters, Larke-Mejía did her PhD looking at the diversity and ecology of microbes that actively consume isoprene, an organic gas mainly produced by trees and other plants that is released into the atmosphere (and is the main constituent of rubber). Now, as part of the GROW Colombia Project, she’s applying the lessons learnt from those past projects to unravel the deep complexities of soil communities in agricultural settings.

“One thing I’ve discovered in my research in the past years is that, if there is a lot of a specific resource, microbes will diversify towards that need,” she explains. “In agriculture, it’s similar, but what you’re adding is fertilisers, herbicides and pesticides.

“The environment is being oversaturated with these chemicals and farmers - without knowing it - are feeding and selecting for certain types of microorganisms in the soil.

“Are these good, are they bad, or just opportunistic microbes in the soil? We don’t know yet.”

Considering the sheer scale of agriculture, the number of different species of microbe inhabiting just a litre of soil, and the diversity of farming practices used worldwide, it’s a monumental task to begin to answer that question. Larke-Mejía therefore proposes a sensible way to approach the problem.

Image: A sugarcane plantation, Cali, Colombia. Credit: Dr. Fernando Muñoz from Cenicaña

Image: A sugarcane plantation, Cali, Colombia. Credit: Dr Nasmille Larke-Mejía

“It’s very difficult for you to test a bunch of different soils and be able to make sense of what they’re telling you. If you take all that information, it gets overwhelming,” she explains. “You need a specific question in mind, and a time frame.

“We have a project on nematicides, which kill the tiny nematode worms which infect and destroy potatoes. The farmer is using just this single chemical.”

Larke-Mejía says that aspect - being able to measure changes due to a single input - makes the project an ideal case study. “We want to compare what the soil was like before it was used, after the addition, how the microbiome has changed, and then - after continuing use - measure what is happening to that soil.”

To answer these questions, Larke-Mejía is using metagenomics. This combines sampling directly from the environment with the latest DNA sequencing technology, which allows you to identify the different microbes present in the soil. Not only do you know they’re there, but you can see what they’re doing.

“We know the chemical composition of the nematocide so we can start looking at the DNA of the microbes in the soil and see what they’re doing in response to the nematocide,” says Larke-Mejía.

“If we know the biochemical route that some microbes are using to break down the nematocide, we can say these organisms could be the ones acting on that specific chemical.”

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The environment is being oversaturated with these chemicals and farmers - without knowing it - are feeding and selecting for certain types of microorganisms in the soil

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Image: Farming on a sugarcane plantation, Cali, Colombia. Credit: Dr. Fernando Muñoz from Cenicaña

Diversity is key to healthy soil

Larke-Mejía is applying similar techniques to look at the differences between the soil of conventional sugar cane farms and that of completely organic systems, which input organic fertilizers such as manure. This, she says, will be more complicated for a variety of reasons.

“With the sugar cane, they add a mixture of chemicals. With a combination it’s more difficult to answer ‘who is doing what?’

“There’s also the fact that the definition of soil health is very blurry. Each soil, from each farmer, needs specific amounts of nutrients to produce acceptable yields of the crop. We can’t have one definition of soil health for everyone, but we can look at the indicators.

“Biologically, we’re likely to start seeing enrichment of microorganisms that are consuming the chemicals from the herbicides and pesticides in the conventionally farmed fields versus the organic, where we don’t expect to see those.

“We’re joining up all this information, along with chemical indicators, physical indicators of the soils, and information about the crops. Farmers might also tell us that with organic practices they get lower yields, compared with the conventional practices. All these components together are essential to tell us what is healthy versus not healthy and the long lasting effects of agricultural practices.

“Which is better for the soil? We’ll have to wait and see.”

For Larke-Mejía, diversity is key. “Soils that are healthier and diverse are more likely to contain microbes that have a wider range of traits and strategies to combat phytopathogens. When everything is the same, like with a monoculture, if a fungus suddenly develops a new strategy and becomes a killer, it can do a lot of harm.

“And this is where it gets even more interesting. By promoting healthier and more diverse soils, taking care of that balance, there’ll be bacteria in there creating antibiotics that will combat whatever fungus is threatening to obliterate everything. Healthy soil and biodiversity are associated with the potential to protect against pathogens.”

We’re only just beginning to truly understand how agricultural practices are affecting the soil microbiome. Larke-Mejía shows us that looking at specific treatments for specific crops is the only way to start unravelling the complexity of it all.

What we discover in the process could go a long way to helping us acknowledge the health of our soils, and perhaps offer ways to ameliorate them before it’s too late.

Peter Bickerton

Article author

Peter Bickerton

Scientific Communications & Outreach Manager