Soil has a microbiome, too Staff and friends of the U.S. Embassy, along with representatives from the City of Tel Aviv, celebrate Earth Day 2012 by planting a garden in the vicinity of the beach at Jaffa Slope Park, on April 20, 2012. (State Department photo/Flickr/blueenayim/iStock)
Soil has a microbiome, too

The Netherlands is home to windmills and clogs. It is also home to intensively farmed cropland. Holland’s small size and large population have meant that the country has historically needed savvy agriculturalists to feed its people. It grows less and less of its own food. So the government has to buy out farmers to return cropland to a wilder state.

This program started several decades ago. That's according to Martijn Bezemer, a biologist at the Netherlands Institute of Ecology. Back then, conservationists would simply stop planting and let the land be, or, they would strip off the top layer of soil and leave the sandy subsoil exposed to the elements. Neither approach met with much success. They waited for a healthy grassland to take hold. But the soil, degraded after decades of high-intensity farming, wasn’t recovering.

The government recruited Bezemer to try and speed up the restoration process. His group began experimenting with the process of inoculating degraded soils with dirt from healthy ecosystems. Bezemer’s group wanted to use healthy microbes to treat a sick ecosystem the way physicians can treat many intestinal problems by transplanting gut microbes from a healthy person into a sick one.

Their initial work in greenhouses and on small plots impressed Machiel Bosch, a nature manager for the government. He was helping to oversee the restoration process in the Netherlands. Several years ago Bosch received a new parcel of land and he invited Bezemer to try his soil microbial transplants on a larger scale.

The results were published in the journal Nature Plants. They revealed that small soil inoculations from grassland or heathland could help determine which plants would colonize the area and thrive in the future. “You don’t get the right plants if you don’t have the right soil,” says Bezemer.

Scoop up a handful of soil. The dirt you hold in your palms forms the basis of the life around you, ranging from the earthworms crawling in your garden to the raptors hundreds of feet in the air. But soil is not just a lifeless pile of earth. Symbiotic fungi, known as mycorrhiza, is living in plant roots. They help the plants extract vital nutrients. Other microbes break down decaying plants and animals, replenishing the materials used by the plants.

Scientists believed that soil microbes were broadly similar around the world. But more recent work has revealed that microbial populations are actually hyper-local. That's according to Vanessa Bailey, a microbiologist at Pacific Northwest National Labs who studies at the foot of Rattlesnake Mountain in Washington State. That soil is actually quite different from the soil at the top. From the foot to the top there is an elevation change of just 3500 feet.

What this means for scientists is two-fold. For one, it means that microbial diversity in soil alone is probably far more immense than anyone had anticipated. “We have the tools now to describe microbes in much greater detail than even five or ten years ago,” said Noah Fierer, a microbiologist at the University of Colorado at Boulder. “Yet 80 percent of the soil microbes in Central Park are still undescribed. There’s a lot of diversity to reckon with.”

The second implication is that two different ecosystems, even those in close proximity, could have very different microbes living in their soil. A plant might survive drought not because of something inherent to its physiology, but because of the assortment of symbiotic microbes in the dirt, Fierer said. Plant the seeds elsewhere, and they may not be able to germinate, grow and thrive without the proper mixture of bacteria and fungi. As researchers began learning more about the depth and complexity of these interactions, Bezemer realized that could explain why his native country’s attempts at returning farmland to native ecosystems was failing.

The process could work, Bezemer believed, if the right soil was present. At first, he tried moving the soil wholesale. It wasn’t a problem for small projects in pots and greenhouses, but scaling any projects up would be difficult, as soil is heavy and hard to move. Still, these early trials gave Bezemer enough data to show that seeds did better when they were planted in soil taken from other ecosystems where those species thrived.

Not only did the plants grow better, but the transplanted soil also prevented weeds and other non-desired plants from dominating the new system before the native species had a chance to take hold.

For Bezemer, the problem with this approach was the amount of soil needed. To adequately convert farmland to grass or heathland across the Netherlands, conservationists would effectively have to strip all of the soil from healthy ecosystems. But if microbes were the important factor, then maybe he didn’t need massive quantities of dirt.

The experiment took six years, but the data clearly showed that the donor soil steered the former agricultural land towards an ecosystem that looked like the original source. Grassland soil created grassland, heathland became heathland. Stripping the topsoil allowed for stronger donor soil effects, and the ecosystems also recovered faster.

Bailey published her own study on how climate change might affect soil microbes, and says that these results show not only the effects of donor soil on ecosystem restoration, but also how competition between soil microbes can affect how plants grow. The likely reason that the inoculations had less of an effect when the topsoil wasn’t removed was competition between the existing microbes and the ones in the transplanted soil.

Soil remains an ecological black box for scientists. Even now, researchers are just beginning to understand how microbes that we can’t even see could potentially shape the world around us.

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