Going underground for soil ecology

Soil is far more than just dirt. Are you nurturing the organisms that help it grow great crops?

A warm, early-July breeze blew through a wheat field in northeastern Saskatchewan, not far from Nipawin. The heads had just emerged and were still green, but the field was taking on that fuzzy look that you typically get with a fresh, bearded cereal.

This field was unusual, however, because even though you couldn’t see it, red clover was sown under the wheat, so there were actually two crops occupying the same space: wheat for harvest this year and seed clover for next.

It’s a strategy that pays off with more biodiversity above the soil surface, and also underneath it.

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Soil ecology is still on the frontier of science. We know quite a bit about what soil does, based on our observations above the ground and our knowledge of a few simple elements: nitrogen, potassium, phosphorus and sulphur. But soil itself isn’t simple and we’re starting to understand we have to look at it not as a simple workbench but as a highly complex factory.

“It’s a very, very diverse ecosystem — perhaps the most diverse ecosystem on Earth,” says University of Saskatchewan soil scientist Jim Germida. “Of course, all those micro-organisms are doing lots of different things in terms of ecosystem services, everything from cycling nutrients through the system and helping clean water to helping plants grow.”

The sheer number of different organisms living in a healthy patch of Prairie soil is staggering. If you count the number of stars that you’ll see on one of those clear western nights where even the edges of the Milky Way are visible as a creamy band down the centre of the sky, that’s about equal to the number of different kinds of organisms living in one teaspoon of that soil.

That’s a lot of living things doing a lot of work within a very small space. This kind of diversity and the genetic variability within their populations is called biodiversity, and it’s essential to the proper functioning of any ecosystem.

In 2010, the European Commission published a major report on soil biodiversity, classifying the work of soil organisms into three main functions. The first are the chemical engineers, made up of organisms that decompose dead tissue within the soil and transform it into the nutrient fuel that drives the system. The second are the soil regulators, including the predators and grazers that manage the populations of other soil organisms. These include our soil borne pests and diseases. The third, then, are the ecosystem engineers, the burrowers and tunnelers that move soil particles around and develop the pore spaces that make water and air infiltration possible.

What this means is that in the course of a year, the soil organisms within the area of a soccer field will process material equal to the weight of 25 small cars. This sort of biological activity is important to soil ecology and has a profound effect on agriculture.

But then, agriculture also has an equally profound effect on soil, points out Dr. Tandra Fraser of the Global Soil Biodiversity Initiative based out of Colorado State University.

Monocultures not only reduce biodiversity above ground, they also reduce biodiversity underneath it, Fraser explains. “Then this leads to a number of problems. Soil biota and microbes contribute to the maintenance of soil structure, they contribute to the hydrological process and to nutrient cycling which, in the end, is related to food production.”

Before the Green Revolution, farmers practised diverse crop rotations. Not only did they change fields from one annual to another, they rotated from annuals to perennials. Perennials keep roots in the ground year round for three or more seasons, conditioning the soil and energizing the soil biota. Since most farms were mixed, sections of land were also used for forage for livestock and the animal manure was used as fertilizer. Above the topsoil they had biodiversity over time and this helped maintain biodiversity below ground as well.

The development of farm chemistry and machinery changed all that. It may be said that the Green Revolution created today’s specialized agribusiness and our rotations of annual crops. Livestock farmers became more specialized as well, and there was a separation of animals from the plants. There was no longer any need to rotate to perennials, and animal manure was no longer available to most crop farmers.

This is the system we’ve been working under for multiple generations and it has its quirks. But the news here isn’t all bad either.

One benefit of farm chemistry is the emergence of zero-till agriculture, where leftover crop residue helps to keep topsoil in place. The remaining roots retain moisture in the ground and provide a source of organic matter, which helps explain why we’ve seen soil condition improve under a zero-till regime.

“The soil organic matter helps with stabilization of the soil,” Fraser says. “It provides the carbon source for the soil micro-organisms. On top of that you need nutrient balance between the carbon, the nitrogen and the phosphorus and the other nutrients for uptake. The reduced tillage since the ’80s has been huge.”

As we change land use from a natural grassland ecosystem into a more intensely cultivated system,  however, we need to understand that we are reduceing soil biodiversity, Fraser says, and we really need to learn more about the ecology of living soil, such as knowing what organisms are in there and what they do in a healthy system.

This is the problem. We really don’t know that much about soil biology and biodiversity. Most soil organisms are microscopic and they live in a dark world that’s very difficult to observe first hand.

“The thing that has changed in more recent time is the fact that we have new tools to help us study biodiversity,” Germida says. “Now we’re talking about using molecular tools where we can extract the DNA from soil or from the roots and we can start studying the microbial communities that are there. We can think about it as a sort of meta-genome of all these living organisms and how they work in concert to do these different beneficial things, just like we have the human microbiome. We have all these micro-organisms living on and in us, and these things are very beneficial and help us be who and what we are.”

If this is the same with soil, then we have a lot to learn about how we can use the subtle nuances of its biology to help grow food. Germida begins by saying we need some optimal equilibrium of different organisms. The right mix makes the whole system more resilient. For example, if moisture levels or the pH changes, one group of microbes may fail but another can step in to continue their work. This can involve any number of things such as mineralizing organic nutrients so plants can use them, decontaminating pollutants, or even controlling certain plant diseases.

Take-all is the Pacific Northwest name for a fungal disease that affects wheat along the west coast. It lives in the soil, infects the plant through the roots, and may infect its neighbours. It affects the conductive tissue and restricts water uptake. Too much of it in the soil, however, provokes an interesting reaction.

“We have this thing called Take-all decline and as the pathogen infects the plant, the plant starts to send out chemical signals that stimulate a certain group of bacteria in the soil,” Germida says. “Those bacteria get very abundant and they actually produce antibiotics against the pathogen and the incidence of disease declines after a period of time.”

In other words, nature doesn’t like an overabundance of pathogens either. Eliminating their predators may have made our crops more vulnerable, but by understanding the relationships between soil chemical engineers, soil regulators and soil ecosystem engineers, we may be able to create a food production system that is more sustainable and that makes economic sense as well.

“I grew up on a conventional farm and I understand it from an economic point of view,” Fraser says. “If farmers are not making money or if it’s going to be a huge expense to them they’re probably not going to change their management strategies.”

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