Archives For soil research

Reforestation from the Ground Up

Undercover Science

Julianne Beck —  August 3, 2016 — 1 Comment

Experts in reforestation are concerned with the reasons why some replanted sites struggle. They suspect the problem may be solved through soil science.

The health of a forest is rooted in soil and the diverse fungi living within it, according to researchers at the Chicago Botanic Garden, Northwestern University, and collaborators at China’s Central South University of Forestry and Technology.

In densely populated places such as the Chicago area and Changsha, the capitol of the Hunan province, ongoing development and urban expansion frequently lead to the deforestation of native natural areas.

Collaborators tour a study site in China.

Research collaborators tour a study site in China.

“There has been a lot of deforestation in China and so there is interest in knowing how best to do reforestation, whether we’re using native plants or introduced plants in plantation settings,” explained Greg Mueller, Ph.D., chief scientist at the Garden. “Understanding who the players are both above ground and below ground helps us understand the health and sustainability of that above-ground plant community,” he added. “It’s analogous to restoration work being carried out here in the Midwest.” The climate, he explained, is similar in Changsha and Chicago.

A wide variety of fungi live in a symbiotic partnership with roots of trees everywhere. These fungi and trees are involved in a vital exchange of goods. The fungi deliver water and nutrients to the trees, and in return take sugars the trees produce during photosynthesis. Without this symbiotic relationship, the system would fail.

Not all tree species and fungi can team up for success, according to Dr. Mueller, who explained that it is essential for the partners to be correct if the tree is to survive. “The wrong fungi may actually be more pathogenic than beneficial,” he explained. Mueller is guiding research on this delicate soil-tree relationship as conducted by his doctoral student Chen Ning.

Ning is on leave from his position as a lecturer at Central South University of Forestry and Technology while he completes his studies with the Garden and Northwestern University. However, much of his work is taking place in China, where he has just completed the first phase of fieldwork.

After completing his master’s degree, Ning was keenly aware of the important role fungi play in the health of the natural world. He knew that he “wanted to ask some questions about the environment and how fungi influence the environment.” He added with a smile, “that’s why I chose to do some dirty work in the soil.”

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Chen Ning stands behind Dr. Greg Mueller and collaborating professors.

The bright scientist is using the latest technology available, next-generation sequencing, to examine the molecular composition of soil samples taken from locations where native or nonnative trees or both were replanted 30 or 40 years ago. Specifically, he is looking at the replanting of Mason pines, a native Chinese pine, and slash pine (Pinus ellitottii), a nonnative pine introduced to China from the tropical state of Florida.

Ning recently completed his first review of those samples, finding large numbers of fungi in each. In addition, he found that the three different habitats have very different fungal communities.

Mueller and Ning visited the university and collaborators in Changsha in February. Mueller was able to visit the sites Ning sampled during the first phase of research and see the setup for the second phase of research in the greenhouses. The level of disturbance in the natural areas was extensive, a point of interest for Mueller who said, “that again makes it interesting to look at some ecological questions about disturbance and how that impacts these systems.” The team also had time to discuss the importance of considering fungi in related research initiatives.

PHOTO: Dr. Greg Mueller and Chinese collaborators.

Taking a break for a selfie and some sightseeing

Next up, Ning will examine his greenhouse plantings that use soils taken from his different field sites to determine if the fungi community changes in response to what type of tree is planted. When that is complete at the end of this summer, Ning will look at the enzyme activity in the soil to determine if fungi are functioning differently in the three different plantings (native forest, native tree in plantation, exotic tree in plantation). The study is on a fast track with a targeted completion date in late 2017 and is expected to add new understandings to the biology of plant-fungal relationships while generating important information on reforesting disturbed sites in south-central China.

After completing his Ph.D., Ning hopes to work as a professor to inspire students in China to pursue similar research. He also aspires to serve as a bridge between the United States and China for new research collaborations on topics such as climate change in order to help figure out the ‘big picture’ in the future.


©2016 Chicago Botanic Garden and my.chicagobotanic.org

The Secret Society of Soil

Undercover Science

Julianne Beck —  December 21, 2015 — 4 Comments

When you lift a rock in your garden and glimpse earthworms and tiny insects hustling for cover, you’ve just encountered the celebrities of soil. We all know them on sight. The leggy, the skinny, the pale…the surprisingly fast.

Behind this fleeting moment are what may be considered the producers, editors, and set designers of the mysterious and complex world of soil—fungi. They often go unrecognized, simply because most of us can’t see them.

PHOTO: Otidea decomposer.

Otidea, a decomposer

Fortunately, new technologies are helping experts, like Chicago Botanic Garden scientist Louise Egerton-Warburton, Ph.D., get a better look at fungi than ever before, and discover vital information.

“One of the problems we have with soil science is that you can’t see into it so you really depend on a lot of techniques and methods to work out what’s happening,” explained Dr. Egerton-Warburton, associate conservation scientist in soil and microbial ecology. 

In the last year, she has used high-throughput sequencing (also termed Next Generation Sequencing) to identify more than 120 species of mycorrhizal fungi in a single plant community. In contrast, previous reports suggested there were, at most, about 55 mycorrhizal species in a plant community. These tiny heroes are microscopic organisms that attach themselves to plant roots, for example, to carry out critical functions that support all life on earth. They are essential for the well-being of more than 85 percent of all plants, including those in your garden.

Mycorrhizal fungi are fungi that have a symbiotic relationship with roots of a vascular plant; from the Greek for “fungus” and “root.”

PHOTO: White mushrooms.

Mushrooms are the above-ground fruiting body of fungi.

If climate change results in more intense rainfall and drought—as is predicted by climate change scientists—mycorrhizal fungi will also play an important role in processing varied levels of water in the soil.

Egerton-Warburton has just returned from November field work in the Yucatán peninsula of Mexico, where she has been testing the responses of mycorrhizal fungi to changes in rainfall and soil moisture, especially to drought. Will fungi be able to keep pace? Will they be able to survive? What does that mean for other plant life? “Fungi are really good indicators of any environmental problems. So they are more likely to show the effects of any environmental stress before the plants will,” she said.

Each type of fungi also has a specific role, according to Egerton-Warburton, with some specialized to take up nutrients from the soil, while others cooperate to complete a function, such as fully decomposing a leaf.  A lot of fungi are needed to keep the system working. “You get 110 yards of fungal material in every teaspoon of soil,” she explained.

Aside from breaking down deceased plant material, fungi play a key role in many plant-soil interactions and the redistribution of resources in an ecosystem. They filter water that runs into the ground, cleaning it before it hits the bottom aquifers and drains out into rivers. Also, in the top few inches of soil, many fungi are respiring, along with their earthworm and other living counterparts, helping to filter gases and air that move through the system. Of growing interest, is also the fact that fungi could have a major role in soil carbon sequestration.

Soil carbon sequestration is the process of transferring carbon dioxide from the atmosphere into the soil in a form that is not immediately reemitted.

PHOTO: Leucocoprinus fungi.

Leucocoprinus fungi

For the past four years, Egerton-Warburton and colleagues at Northwestern University have been working to better understand the flow of carbon through fungal communities that results in long-term soil carbon sequestration. Soil’s capacity to store carbon is a reason for hope and a potential way to mitigate climate change. According to Egerton-Warburton, soil is known to hold three times more carbon than plants and trees above ground. “Maybe there are other ways we can manage the systems and enhance that capacity in the soil,” she said.

The study has required a lot of ‘getting to know you’, as the researchers first sought to identify each type of fungi involved in the process of carbon sequestration. As plant parts above ground are faced with absorbing and converting larger and larger amounts of carbon dioxide from our atmosphere into sugars, and sending it down into their roots, the more beneficial it will be to have a healthy suite of fungi waiting to receive it, use it, and move it along for future long-term storage.

Part of this equation has been to understand which fungi benefit from the increasing supply of sugar. Previous work by Egerton-Warburton has shown that mycorrhizal fungi respond to increases in atmospheric carbon dioxide by producing large quantities of hyphae, a fine root-like structure, in the soil. This is because increases in atmospheric carbon dioxide allow a plant to produce more sugars during photosynthesis, and these sugars are shunted below ground for use by roots and their mycorrhizal fungi. At the other end of the equation are saprophytic and decomposer fungi, waiting to break down the new hyphae.

Recent work in the Dixon Prairie has used the high throughput sequencing and chemical fingerprinting to identify the fungi involved in this decomposition phase. Once that is resolved, they will be able to better understand how the fungi interact and balance the cycle carbon through specific pathways of activity.

Learn more about soil science in the winter 2015-16 issue of Keep Growing, pages 28-30.

PHOTO: Louise Egerton-Warburton.

Louise Egerton-Warburton at work in the soil lab

The more the merrier, when it comes to fungi, and when it comes to people who are willing to help them endure, said Egerton-Warburton. The scientist often works with students who are interested in careers in the field, but encourages additional people to consider this critical line of work. “There’s a real need for soil ecologists in the country,” she said.

The good news is that the future story of fungi is one we can all help to script. Gardeners, she advised, can pay attention to the type of mulch they use in their garden, and plant lots of native species that will naturally enrich the function of that wonderful world that holds us up.


©2015 Chicago Botanic Garden and my.chicagobotanic.org