Ecology goes underground

The functioning of terrestrial ecosystems seems to depend heavily on soil biodiversity. But what controls this diversity, and how will it fare in the global greenhouse? Jon Copley digs for some answers.


What are the most poorly researched habitats on Earth? Remote environments such as volcanic vents on the ocean floor or lakes hidden under Antarctica's ice must feature prominently on the list. But it might come as a surprise to learn that some ecologists would also include the top metre of dirt in your garden. Terrestrial ecologists have always given at least some thought to the chemistry and physical structure of the soil. But only recently have they begun to understand that soil biodiversity is a crucial factor in regulating how ecosystems function.

Over the past few years, ecologists have realized that many of the most important interactions between plants take place below ground — particularly in the third of the world's soils that are poor in nutrients. In such soils, the dynamic interactions between plant roots, animals and microbial processes seem to determine what grows where and how. But ecologists have barely begun to study the biodiversity that underpins these interactions. And this ignorance is worrying, as it means nobody can predict how soil biodiversity — and hence the function of terrestrial ecosystems — will be affected by the build-up of greenhouse gases in the atmosphere. Next week, at the Ecological Society of America's annual meeting in Snowbird, Utah, society president Diana Wall of Colorado State University in Fort Collins will call for a major expansion in soil ecology research. “There aren't enough studies out there and they could be multiplied many times over,” she says.

Slice of life: plant roots, seen in section right, are at the heart of dynamic interactions in the soil. Credit: J. C. REVY/SPL

As ecologists have begun to pick up their shovels, they have been faced with a huge challenge: a single cubic metre of temperate grassland soil contains thousands of species of microorganisms and invertebrates whose identities and activities are largely unknown. “There is ecology that is as complex as any of the community and ecosystem ecology that has been studied above ground,” says David Tilman of the University of Minnesota in St Paul. Tilman's Minnesota grassland study was instrumental in confirming the link between high biodiversity and both the stability1 and productivity2, in terms of biomass and carbon turnover, of terrestrial ecosystems. But those studies only considered above-ground biodiversity, and Tilman is now turning to the soil in an attempt to understand the real dynamics of his grassland ecosystem.

Turf accounting

Two of the main current projects focusing on soil biodiversity can trace their origins to a summit of British and American ecologists held in 1994 at the Natural History Museum in London, which discussed the need to rectify ecology's subterranean blind spot. In 1998, Britain's Natural Environment Research Council (NERC) started a £6 million (US$9 million), five-year research programme, centred on a field site at Sourhope in southern Scotland. Wall, meanwhile, heads a parallel US project, launched in the same year by the National Science Foundation and funded to the tune of $1.8 million over four years. This is based at a long-term ecological research site at Konza Prairie in Kansas — with some sampling also taking place at Tilman's site at Cedar Creek in Minnesota.

Even before these projects were launched, some ecologists were turning to the tools of molecular biology in an attempt to unlock the secrets of soil diversity. Molecular probes soon revealed that the soil contains many more microorganisms than can readily be cultured3. Now, ecologists are trying to work out which of these microbes is doing what. “The problem with soil microbiology is that you don't know which organisms are doing which job,” says Phil Ineson of the University of York, a prominent figure in the NERC soil biodiversity programme.

To tackle this problem, Ineson and his colleagues devised an approach based on the fact that when bacteria copy their DNA before dividing, the new strands of DNA incorporate carbon derived from whatever organic compounds the microbes have been digesting. So by adding particular organic compounds labelled with carbon-13 to bacteria in soil extracts, only those that can break down the compounds should incorporate this heavy isotope into their DNA. Thanks to this weighty DNA, these bacteria can then be separated out by centrifugation, and their DNA sequenced to identify them4. “You can characterize the organism that is actually doing the functional business,” says Ineson. In May this year, his team demonstrated that a related technique — using gas chromatography and mass spectrometry — could isolate and classify soil bacteria that oxidize atmospheric methane labelled with carbon-13 by detecting the heavy isotope subsequently incorporated into the bacteria's membrane phospholipid fatty acids5.

Making the earth move

Shahid Naeem.

Other researchers are applying more traditional ecological methods to the problem of soil biodiversity. Experimental manipulations such as removing starfish from a stretch of rocky shore, or excluding sheep from a section of hillside, are relatively easy to do — but controlling the denizens of the soil in a similar way is extremely difficult. “There's no way to radiocollar a bacterium, or to build a cage to keep it out,” observes Shahid Naeem of the University of Washington in Seattle, who is examining the microbial ecology of soil from Tilman's plots of Minnesota grassland. “No one can really manipulate bacteria in a natural system, so you usually bring it into the lab.”

This is exactly what Hefin Jones of Cardiff University and John Lawton, chief executive of NERC, are doing. Using soil from Sourhope, they have set up systems with three different levels of diversity in a facility called the Ecotron. Based at NERC's Centre for Population Biology at Imperial College's outpost in Silwood Park, west of London, the Ecotron is a series of experimental chambers in which conditions can be manipulated according to the whim of the investigator6. Jones and Lawton have set up systems at three different levels of diversity, based crudely on the maximum size of the organisms present. Only microorganisms are present in some chambers, whereas others contain microorganisms plus small invertebrates such as springtails and mites. A third set of chambers contain all of the soil biota including larger invertebrates such as earthworms.

Intimate links: the hyphae of an arbuscular mycorrhizal fungus within the root of a plant. Credit: ALASTAIR FITTER

The chambers were set up three months ago and the plants will soon be dosed with carbon dioxide labelled with carbon-13 to trace the path of carbon through the different organisms. Mid-way through the 18-month experiment, one half of the microcosms at each level of biodiversity will also be ‘shocked’ — by adding fertiliser, for example — to see how resilient the systems are to perturbation. Given the rich web of interactions possible between the various soil inhabitants for each treatment, the experiments may well yield more questions than answers. But the results should start to give ecologists a better understanding of the relationship between soil biodiversity and ecosystem function.

‘Mycorrhizal’ fungi are among the key players in soil ecology. They envelop — and in some cases penetrate — plant roots, and help the plants to acquire hard-to-obtain nutrients such as phosphorus from the soil. In return, the fungi receive carbon from their plant hosts. “If you stand upside down, as it were, and put your head in the soil, you'd think the interesting organism here is the fungus,” says Alastair Fitter of the University of York. “There is very good evidence to suggest that the early land plants were only able to grow on land because they were symbiotic with these fungi.”

Root of the problem

Mycorrhizal fungi grow through the soil, colonizing the roots of various plants and sometimes forming links between them. In the case of trees colonized by ‘ectomycorrhizal’ fungi — which surround but do not grow into plant roots — carbon can be transferred from one tree to another through the fungi7. ‘Arbuscular’ mycorrhizae, which actually grow into the roots, forming intimate connections with their cells, influence the diversity and productivity of plants in the soil they inhabit8 and protect them from pathogens9. They also release a glycoprotein that affects the physical structure of the soil, seeming to boost its stability10. But the structure and dynamics of these fungal communities are only just beginning to be uncovered. “They are exceptionally important and exceptionally poorly understood,” says Fitter. “Because we are above ground, we think from an above-ground perspective. We've forgotten that there is another type of organism down there.”

High turnover: earth dwellers such as this mite move carbon into the soil. Credit: CUSTOM MEDICAL STOCK/SPL

Because they depend on their plant hosts for carbon, mycorrhizae also play an important role in moving the element very rapidly from plants into the soil ecosystem. Fungal filaments, or hyphae, containing carbon obtained from the plant hosts, extend out into the soil and “are immediately going to be gobbled up by every mite, springtail, or whatever there is out there”, says Fitter.

To investigate this carbon flow, Ineson and his colleagues have used some 3 kilometres of plastic tubing to pipe carbon dioxide labelled with carbon-13 to plants growing on plots at Sourhope. “We're finding out where the carbon goes, tracking it into mites, earthworms and all the other things,” Ineson explains. The researchers have already seen the carbon-13 move swiftly from the plants into the soil11. “Within 30 hours it's gone through the plant,” says Ineson. “It goes into the mycorrhizae very quickly and then out into the soil system.”

That sinking feeling

Experiments such as this could prove extremely important in providing baseline information from which to investigate how ecosystems will respond to rising levels of greenhouse gases. Soil is an important reservoir for carbon, containing around 1,500 gigatonnes (1,500×109 tonnes) globally. At present, it is also a net sink for carbon, absorbing more from the atmosphere than it releases. The big question is what will happen as levels of atmospheric CO2 rise. How will this affect soil biodiversity? And if this diversity is perturbed, could the soil cease to be a carbon sink? If so, the effects would be dramatic. “There would be another 2 gigatonnes of carbon accumulating in the atmosphere every year,” says Fitter. In the 1980s, the amount of CO2 in the atmosphere was rising by about 3 gigatonnes a year — so the collapse of the carbon sink in the soil could potentially wipe out current efforts to reduce greenhouse gas emissions.

In an attempt to answer these questions, Fitter and his colleagues have looked at the effects of elevating levels of atmospheric CO2, growing turf from a field site on Great Dun Fell in Cumbria, northwest England, in specially designed glasshouses called ‘solardomes’12. “The excitement was below ground,” says Fitter. The biomass above ground was unaffected, but when CO2 levels were raised from 350 to 600 parts per million, the researchers found root biomass increased by up to 50%. The turnover of root growth and death also went up.

Jones, meanwhile, has looked at the effects of elevating CO2 to similar levels on communities in the Ecotron. As with Fitter's study, the action was underground. “We saw some changes above ground, but the major effects came through in the soil,” he says. The species of fungi present changed, with those that digest cellulose becoming more dominant, and total numbers of springtails increased dramatically13. “As the animals depend so much on the fungi, changes in the fungi result in changes in soil fauna,” Jones explains.

A state of flux

The significance of these changes for carbon flux is not yet clear. Says Jones: “If we believe the soil to be quite a big sink for carbon, do changes in soil biota change the amount of sink?” Fitter agrees that it is unclear whether changes in soil ecology caused by elevated CO2 will speed up the carbon cycle or slow it down. Higher levels of CO2 in the atmosphere could lead to a higher ratio of carbon to nitrogen in the soil. Leaf litter with a high carbon-to-nitrogen ratio generally decomposes more slowly, which could slow the release of carbon from the soil, allowing it to accommodate more carbon from the atmosphere over time. If so, the result could be a form of negative feedback that would put a brake on global warming.

But few ecologists are willing to bet on this happening. “Quite a few experiments suggest that effect, but others show the opposite, so when you put all the data together there is no overall significant effect,” says Ineson, who is compiling a review of studies looking at the effects of elevated CO2 levels on soil carbon flux. “We can't rely on soil to sequester more carbon under elevated CO2 — this is not the answer to the problem of global warming.” Indeed, higher temperatures themselves could cause problems. When Fitter and Ineson experimentally warmed the soil at Great Dun Fell by 3 °C for up to 18 months at a time, they found a hugely increased rate of decomposition14. This would reduce the soil's ability to act as a store for carbon, potentially exacerbating global warming.

Ecologists working on the problem of soil biodiversity and carbon cycling argue that there is an urgent need for more studies. “We have not yet got the answers to the questions that are going to be so important on a global scale,” says Ineson. Without this information, current efforts to limit climate change under the Kyoto Protocol by haggling over land use and trading of ‘carbon credits’ might be based on shaky foundations. The soil, concludes Ineson, can no longer simply be trampled underfoot. “Suddenly it's coming into the political arena.”


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Copley, J. Ecology goes underground. Nature 406, 452–454 (2000).

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