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Cover crops – the solution to healthy soils?

Cover crops can improve soil health, but there’s a catch. Anglia Farmer’s Judith Tooth talked to soil ecologist Marco Fioratti Junod to find out more.

The benefit to soil health of growing cover crops is at least partly offset by cultivations. That’s the initial finding of research by soil ecologist Marco Fioratti Junod at the John Innes Centre.

“Sadly there are no easy answers,” says the postgraduate researcher, whose study is an industrial partnership funded by John Innes Centre, the Biotechnology and Biological Sciences Research Council, Syngenta and the University of East Anglia, with external support from NIAB. “Cover crops are useful, but they are not a silver bullet to restore soil health. They are good in ecological terms, but if farmers need to cultivate the soil, it could take years to get a positive effect.

“In theoretical terms you could get the maximum benefit from cover crops with no-till – and the richest and most resilient soil is one not destroyed by cultivations every year. But agronomy is complex.”

In the field research

In his third year of research, supervised by John Innes Centre senior scientist Professor Tony Miller, along with Professor Brian Reid from UEA and Dr Ian Sims at Syngenta, Marco has now collected nearly all the data he needs to begin writing his thesis, which has the working title, ‘Investigating the effect of cover crops on below-ground biodiversity’. What marks his study out from many others is that it has been carried out in the field, rather than in the sterile conditions of a laboratory or greenhouse.

“If you enrich soil in a greenhouse with springtails, soil mites and so on, you get substantial changes in how, for example, ammonium is oxidised, or how much leaching occurs. But studies tend to be carried out in conditions that are as sterile as possible, and so soil organisms are often overlooked.

“So I’m taking soil fauna into account, which adds a lot more noise and complexity, because what happens in the soil is as complicated as what’s on the surface – but any findings can be immediately and directly applicable to a real life crop.

“By enhancing our understanding of this really complex trophic chain we might one day be able to engineer soil communities by adopting suitable agricultural practices that enhance instead of degrade the soil.”

Trial sites

While the focus is on cover crops, they can’t be analysed in isolation because they are used as part of farmers’ cropping rotations. So Marco has had three trial sites: a crop of winter wheat following a cover crop at the John Innes Centre’s field station at Bawburgh; a cultivations and rotations trial at The Morley Agriculture Foundation, a herbal ley following arable cropping at a site at Otley in Suffolk.

The traditional way to sample soil is to take a soil core, and, using a mixture of light and heat, extract all the organisms from it in a laboratory. It’s simple, but expensive. So Marco has devised a different method, which involves removing a core of soil with an auger and replacing it with a simple tube with a screw top. The tubes, partially open-sided, remain in place across the three sites for the duration of the trials – except for a brief period during cultivations – and invertebrate samples are collected from them at regular intervals.

Research at the field at Bawburgh began in spring 2019, when the trial area was divided into 18 plots measuring 6m x 6m, with an additional three plots in the field margin. (Marco works on a further 15 plots at Otley and 48 at Morley.) Following the previous cereal crop, six were sown with a legume, clover and cocksfoot cover crop, six with radish and six left as bare fallow. The cover crops were terminated using glyphosate, replicating what most farmers use to prepare the ground, before cultivating the soil lightly and drilling winter wheat. From spring this year, the area was subdivided further, with each plot receiving either the recommended rate of nitrogen, or none.

“I’ve been collecting samples every two months. I’m interested in the soil fauna in the top 20cm of the soil, but the tubes could easily be modified to make them deeper, for example. Bacteria can be identified in DNA sequence reads, and more reads means greater abundance. But the same does not apply to invertebrates, and we don’t yet have good libraries to use as a reference for identifying mesofauna, even though it is possible to put the sample in a blender and extract their DNA. So I’ve been identifying the organisms under a microscope.”


Mesofauna, such as springtails and mites, not visible to the human eye, come between microfauna – fungi and bacteria, and macrofauna, such as ground beetles and earthworms, in terms of size.

“There are hundreds of species of mesofauna, and little is known about what individual ones do. We’re scratching the surface, really, and it’s very difficult to isolate the effect of a single species. But we can establish if there are significant differences, and we can look at the effect of cover crop residues, and the communities feeding on them.

“We can see that cover crops have the potential to shape very different below ground assemblages, and that these can determine how much nitrogen is available to the crop.”

Seasonal change

Marco has identified different soil communities across the trial plots. There is a lot of seasonal change below the surface, including in the field margin: many beetles hatch in autumn, for example; springtails are common all year round; some organisms prefer wet conditions and others, dry.

Those enriched with nitrogen have fewer fungal feeding organisms. But mechanical soil disturbance is the main way communities are depressed. At Otley, for example, where the herbal leys were established following either ploughing or non-inversion, the difference is still apparent two years later.

“Intensity of tillage is the main driver. It takes years for the soil to recover, and is particularly true for larger organisms such as earthworms, but the difference is reflected across all soil fauna.”

In nature, says Marco, all processes in the soil are mediated, catalysed or provided directly by soil fauna: they can open up the soil, improve its structure, its infiltration, its resistance to erosion; they can balance pH and nutrient levels, make nutrients available to plants when the plants need it, and even provide weed and pest control. But in arable farming, many of these services are provided artificially. The difficulty is that doing this dramatically affects the services soil could otherwise provide.

“It’s soil micropore formulation by earthworms versus ploughing, mycorrhizal fungi versus fertiliser application, and so on. In other words, the things in the soil that would do the same job are repressed.

So if we understand a bit more, then we can harness more of what the soil can offer, with ecological and economic benefits.”

This article originally appeared on Anglia Farmer and is re-produced here with permission.

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