Surviving Serpentine Soil

Recently published in Nature Genetics, a paper by Sergey Nuzhdin, alumnus Tom Turner, and their co-researchers reveals how plants survive in marginal soil environments.

Nuzhdin, professor of molecular biology in USC College, and his colleagues made two significant and surprising discoveries in their paper “Population Resequencing Reveals Local Adaptation of Arabidopsis Lyrata.” First, dozens of genes are responsible for allowing the plants to survive in marginal soil environments, and not just one or two genes — a re-sequenced whole genome; and second, functional adaptation occurs, which is often difficult to tell apart from selective, pure demographic processes.

But rather than tap into a specialized encyclopedia to understand biological terms, Nuzhdin crafts an analogy about people to enhance the understandability of the study. He begins with an observation that you might not think about very much, if at all: “Plants are different from animals; they are stuck at the place where their mom puts them,” Nuzhdin said.

While humans and other creatures come and go as they please, plants cannot. And, some environments are more conducive to their livelihood than others. Nuzhdin and his colleagues focused on the Arabidopsis Lyrata plant, which is an ideally suited plant for population genetic studies.

Sergey Nuzhdin is professor of molecular biology in USC College.

Lyrata thrive in the serpentine soil of California and other parts of the world including Scotland where co-researcher Elizabeth Bourne lives. Serpentine soil, characterized by high levels of heavy metals and low levels of important plant nutrients, is mottled green like the snake that bears its name. Serpentine rock of similar hue is pervasive in California and is the official rock of the state of California.

Some plants have difficulty surviving Serpentine soil due to its various concentrations of ions that do not transfer correctly between cells and between soil and cells. One of the key questions researchers ask is what has changed to make these plants adapt to the soil? According to Nuzhdin, the traditional experiment would take 10 to 15 years, but you can take shortcuts by identifying similar molecular variations that occur in other locations.

“Suppose you have people in Los Angeles and the Central Valley and both groups can deal with stress,” Nuzhdin said. “They share the same genos and variations that allow them to handle stress. Then you take samples to see which genos are different and which are the same. What you will find is that some genes are not mixing between the two.” Replace plants for people in this example, but keep in mind that people can move out of Los Angeles if they can’t handle stress. Plants cannot.

Next, the researchers implicated their findings in multiple cases: Los Angeles versus Central Valley, New York versus Long Island, and so on. Bourne identified plants from the same types of soils with the same mutations and molecular variations as those responsible for the adaptation in California.

“If you see consistent differences as we did, then you can speak about selection that is responsible for the differentiation,” Nuzhdin explained

Nuzhdin’s research collaborators included Tom Turner Ph.D. ’09 now an assistant professor of ecology, evolution and marine biology at the University of California, Santa Barbara. Other co-researchers include Elizabeth Bourne, The Macaulay Institute, Aberdeen, United Kingdom; Eric Von Wettbergs, University of California, Davis; and Tina Hu, University of Southern California.