A close-up image of hyphae networks in a soil experiment at the University of British Columbia. Julia Maddison, Flickr

Can soil inoculation accelerate carbon sequestration in forests?

Newly popular field of soil microbiome restoration research offers hope

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When foresters first tried to plant non-native Pinus radiata in the southern hemisphere, the trees would not grow until someone thought to bring a handful of soil from the native environment. “They didn’t know it then, but they were reintroducing the spores of fungi that these trees need in order to establish,” Colin Averill, ecologist at The Crowther Lab, explains. “When we plant trees, we rarely ‘plant’ the soil microbiome. But if we do, we can really accelerate the process of restoration.”

That process of restoration has become one of humanity’s most urgent missions. In order to slow global warming, we know that we need to decarbonize our economy and start removing carbon from the atmosphere – and we’ve largely been looking at doing so through dreams of negative emissions technologies and schemes of tree-planting.

But only very recently has more attention been turned toward another major potential tool for carbon capture: soil. An astonishing 80 percent of the carbon stored in terrestrial ecosystems is stored underground. According to the 4 per 1000 Initiative, a modest and achievable increase in soil carbon of 0.4 percent could be enough to stop the increase of carbon dioxide in the atmosphere.

Pinus radiata seedlings sprouting up from soil in Hawaii. Forest and Kim Starr, Flickr
Pinus radiata seedlings sprouting up from soil in Hawaii. Forest and Kim Starr, Flickr

This is why scientists are beginning to change the narrative around soil through more devoting more research to this crucial part of ecosystems. In the words of Toby Kiers, an evolutionary biologist at Vrije Universiteit Amsterdam researching underground trade patterns, “We’re turning this ‘phyto-centrism’ on its head. What you see above ground is just a detail of what’s happening below ground.”

Just as the microbiota in our guts digest food, fight infection and even make us happy, we are now learning that the microbiota in the soil plays a similar leading role for plants. Welcome to the wonderful world of the soil microbiome.

Mycorrhizal fungi calling the shots

Most people imagine that tree or plant roots burrow into the ground and suck up nutrients, but that is not really what happens. Instead, the roots of most plants enter into a symbiotic relationship with mycorrhizal fungi, and it is these fungi that burrow into the soil, break down its nutrients and ship them back to the tree or plant. But the fungi do not do this for free: they are paid with the carbon that is photosynthesised by the plant, which the fungi use to grow their networks.

“The fungi are so dependent on the plant for carbon that you could say it makes for a power imbalance toward the plant – but I wouldn’t be so sure,” says Kiers. “Fungi can control the nutrient uptake mechanism of the plant and make the plant completely dependent on them for their nutrients.”

“We need to focus on understanding those dynamics and stop viewing mycorrhiza as passive pipes and more as powerful actors who are calling the shots,” she says.

A digital mapping of the underground architecture of microbiomes. Courtesy of Toby Kiers
A digital mapping of the underground architecture of microbiomes. Courtesy of Toby Kiers

Kiers and her team study the trade relationships between mycorrhizal fungi and their plant hosts and have noticed that some fungi make better “deals” than others: they are more stingy with their phosphorus and nitrogen and extract a higher carbon price from plants. If scientists could figure out the perfect “economic” conditions to make nutrients more “expensive,” then the potential for increasing below ground carbon storage is huge.

But Kiers is cautious: “I’m not one to suggest that we should tinker with nature, but you can imagine that this system could be ramped up in such a way that plants have to be more generous with their carbon, and therefore a lot more carbon is sequestered.”

Arbuscular mycorrhizal networks around the world currently sequester around 5 billion tons of carbon per year – that is the same as the annual carbon emissions of the E.U. and Russia put together. For Kiers, the challenge is clear: “The big question in my field is: what scale can we increase that to?”

Scaling up from microbiome experiment to ecosystem

This video, shot in Kiers’ laboratory, shows the flow of nutrients inside a tiny corner of a hyphae network, each “pipe” about half the diameter of a thread of cotton.

“The flow inside these open pipe networks is moving fast and in really complex patterns,” Kiers says. “We’re trying to understand what’s happening in these networks underground and whether we can control those flows. Can we make them speed up? Can we make them go more in one direction, so the plants get more nutrients? These micro-scale decisions and strategies of the fungus are going to have huge ecosystem level effects.”

In just one tablespoon of forest soil there are millions of hyphae, layered in networks almost unfathomably complex. Because of the sheer size of the global mycorrhizal networks, even miniscule increases in soil carbon drawdown could have a huge overall impact.

Kiers and her team are now developing an imaging robot that can follow 40 networks simultaneously, but the trouble, as ever, is taking these laboratory discoveries and translating them to the ecosystem level.

Transforming ploughed cropland to thriving heathland

One of the ways we might increase the amount of carbon in our soils is by transforming agricultural land into forest or heathland. But when a field has been farmed for decades, this transformation needs more than a handful of seeds. Remember what happened when foresters tried transplanting Pinus radiata to the southern hemisphere? Different plant species form symbiotic partnerships with different fungal species.

The problem with re-foresting arable fields is not necessarily that the land is exhausted. In much of Europe, China and the U.S., extensive use of fertilizers means that the soil is often relatively rich in nutrients. However, decades of ploughing will destroy the critically important underground hyphal networks. As a result, these damaged mycorrhizal networks can only support early successional plants: weeds.

Weeds are not famed for their promotion of biodiversity or carbon capture. It is the late successional plants, like those found on mature heathland or forest, that are associated with a rich variety of species and greater carbon sequestration. With time, the communities of fungi and plants on former agricultural land will gradually move through the successional sequence. As the underground fungi diversify, so too would the above ground species, and we would see the farmland slowly transition from weedy scrubland to mature heathland or forest.

However, Jasper Wubs, an ecologist working on sustainable agroecosystems at ETH Zürich, explains that this successional sequence can take 30 years or longer. Back at the start of his research on this topic, Wubs wondered whether there was a way to speed up the transition from ploughed field to thriving ecosystem by introducing fungi from more mature landscapes. “We thought, what if we inoculate the soil with microbes from the late stage and short-circuit the whole process?”

In 2006, Wubs and his collaborators launched a field experiment on former arable cropland in the Netherlands. They collected two different soil samples from land further along the successional sequence: one from a centuries-old dry heathland and another from a grassland restored 24 years earlier. In total, the team inoculated four different plots in the field, simply by spreading a thin layer of the mature soil inocula, either directly over the topsoil or onto bare earth after removing the fertilizer-rich topsoil.

From Wubbs' 2016 study, photographs of two treatment plots, taken eight years after the start of the microbiome experiment. The top control plot was not treated with soil inoculation, while the bottom plot was inoculated with heathland soil. Courtesy of Jasper Wubbs
From Wubs’ 2016 study, photographs of two treatment plots, taken eight years after the start of the experiment. The top control plot was not treated with soil inoculation, while the bottom plot was inoculated with heathland soil. Courtesy of Jasper Wubs

Six years later, Wubs returned to find out what had happened. The resulting study, published in 2016, found that inoculation had not only accelerated the restoration of the ecosystem, skipping over the weedy phase, but had also steered the plant community toward either heathland or grassland species, depending on where the soil inocula originated.

“These experiments show that microbes help determine the fitness of different species and their relative competitive ability, and that determines what the vegetation will look like,” says Wubs. “You cannot really skip thirty years, but you get to a much more interesting point of succession quite fast.”

The importance of symbiotic partnership

Colin Averill, the researcher inspired by the Pinus radiata story, is a microbial, mycorrhizal and ecosystem ecologist at the Crowther Lab, hosted at ETH Zürich. In a study currently in review, Averill was part of the Crowther Lab team that used DNA sequencing of fungal communities in hundreds of forest monitoring plots to unpack the contribution of the soil microbiome to tree growth. Averill summarizes what happened: “We identified fungi that are linked to a three-fold increase in tree growth rate, brought these fungi back into the lab and recapitulated the effects in seedlings.”

Now, Averill is applying this knowledge in two randomized controlled reforestation trials: one in Wales, in collaboration with The Carbon Community, and another on the Yucatan Peninsula in Mexico, in collaboration with the tree-planting organization Plant for the Planet. In essence, this new study is examining how the composition of fungal communities can affect the functioning of entire forests – just as Toby Kiers and Jasper Wubs predicted.

The nine-hectare field experiment in Wales is pasture that has been grazed for centuries. “We know from DNA sequencing that the microbial communities in these agricultural landscapes look nothing like those of intact forests,” explains Averill. “There are a lot of reasons to believe that actively inoculating this land with soil microbial communities might really enhance forest recovery.”

“You can think of it as a randomized controlled drug trial,” he says. “Half the trees get a ‘placebo dose’ of soil from the site we’re planting them into already, and half get a ‘treatment dose’ of soil from a nearby ancient woodland.”

Grassland fungi in in the Glyncornel region of Wales. Dr. Mary Gillham Archive Project, Flickr
Grassland fungi in in the Glyncornel region of Wales. Dr. Mary Gillham Archive Project, Flickr

The trees are being planted in Wales this spring, and a team of researchers will monitor tree growth, carbon capture and, importantly, tree survival rate. For example, Ethiopia hit the headlines in 2019 when citizens planted 353 million seedlings in a single day as part of Prime Minister Abiy Ahmed “Green Legacy” project. But all that hard work could be wasted if the seedlings don’t thrive because of poor soil.

“There’s strong reason to believe that the trees [in unsuccessful tree-planting projects] may be missing their microbial partners, especially when they’re planted in degraded, ex-agricultural landscapes,” explains Averill. “Many trees can’t establish in the wild at all, if their symbiotic partners are missing.”

“We don’t know what we’re losing”

Scientists around the world are now hurrying to explore the biodiversity of the soil microbiome, finding micro-organisms that confer remarkable powers on plants. In 2018, for example, a team from the University of Texas inoculated switchgrass with more stress-tolerant fungi, making the plant itself more resistant to drought.

“Fungi are really valuable – nearly all of our antibiotics come from soil fungi,” Averill says. “But they also represent tremendous chemical biodiversity in the ways different organisms solve problems.”

With each new discovery, it becomes ever more apparent that we ignore the soil microbiome at our peril. Human activity has already had a huge impact on our underground carbon sink. A 2018 study estimated that grazing and cropland cause our soils to store 133 billion tons less carbon than they would in a world without agriculture.

“What happens if soil temperatures increase?” Kiers asks. “Maybe the fungi can survive, but if the nutrient flows inside the mycorrhizal networks go down, even slightly, then that’s going to have major upstream impacts on the ecosystem.”

But if scientists and farmers can collaborate to shift the balance of nutrient flows in favor of carbon sequestration, perhaps we could slow the effects of climate change. “We almost never talk about conserving microbial communities, but they are a huge component of any ecosystem,” Averill says. “We really don’t know what we’re losing.”

A crisis like a rapidly warming planet needs ingenious problem solvers. We might just find them in the ground beneath our feet.



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