A brand new study analyzed soils collected in Kansas to look at the role of “legacy effects,” which refers to how the soil at a given site is formed by microbes which have adapted to the local climate over a few years.
“Soil bacteria and fungi and other organisms can actually have significant effects on things that matter, like carbon sequestration, nutrient movement and what we're particularly interested in—legacy effects on plants,” said co-author Maggie Wagner, associate professor of ecology and evolutionary biology on the University of Kansas.
“We got interested in this because other researchers, for years, have been describing a way for soil microbes to have this kind of environmental memory from their ancestral past,” he said. “We thought that was really interesting. This has a lot of important implications for how we can grow plants, including things like corn and wheat. That in itself has a huge impact on how plants grow, but the memory of the microbes that live in these soils could also play a role.”
According to Wagner, legacy effects have been observed before, though the small print are unclear. A clearer picture could eventually help farmers and agricultural biotechnology corporations aim to harness helpful microbes.
“We don't really understand how legacy effects work,” he said. “Like, which microbes are involved at the genetic level, and how does it work? Which bacterial genes are being affected? We don't even understand how this climate legacy moves through the soil to the microbes, and then eventually into the plants.”
The team sampled soils from six sites in Kansas, spanning the wetter eastern region within the west to the upper, drier high plains, which receive less rainfall due to the Rocky Mountains' rain shadow. The goal was to match how legacy effects vary along this climate gradient.
“It was a collaboration with a team at the University of Nottingham in England,” Wagner said. “We split the work, but most of the experiment — actually, the whole experiment — was done here at KU, and we also focused on the Kansas soil for that work.”
At KU, Wagner and colleagues assessed how these soil microbial communities affected plants.
“We used a kind of old-school technique, treating the microbes like a black box,” he said. “We grew plants in different microbial communities with different drought memories and then measured plant performance to understand what was beneficial and what wasn't.”
The researchers exposed the microbial communities to either abundant water or very limited water for five months to strengthen contrasting histories of moisture availability.
“Even after thousands of bacterial generations, the drought memory was detectable,” Wagner said. “One of the most interesting aspects we found is that the microbial legacy effect was stronger with plants that belonged to these exact locations than with plants that were from elsewhere and were planted for agricultural reasons but were not native.”
To begin examining how plant identity interacts with microbial inheritance, the team compared a crop (maize) to a native grass (gammagrass). They note that additional species will probably be needed to substantiate the pattern, yet preliminary results suggest that native plants may align more strongly with local microbial histories.
“We think it has something to do with the co-evolutionary history of these plants, meaning that for a very long time, gammagrass has lived with these exact microbial communities, but corn has not,” he said. “Corn was domesticated in Central America and has only been in the area for a few thousand years.”
Beyond plant performance, researchers examined gene activity in each microbes and plants to explore potential mechanisms behind heritable effects on the molecular scale.
“The gene that excited us the most was called nicotinamine synthase,” Wagner said. “It produces a molecule that is useful primarily for plants to acquire iron from the soil but has also been recorded to affect drought tolerance in some species. In our analysis, the plant expressed this gene under drought conditions, but only when grown with microbes with memories of dry conditions. The plant's response depends on the memory of the microbes, which we find interesting.”
Wagner noted that gammagrass is being regarded as a source of useful genes for improving corn under stress.
“The genes I mentioned earlier may be of interest,” he said. “The focus for biotech firms on microbial enhancement of crops is where the search for microbes with beneficial properties is. Microbial commercialization in agriculture is a multi-billion dollar industry and still growing.”
Wagner's KKU colleagues were lead authors Nicole Gannon, now of Riverside University in California, and Natalie Ford, now of Pennsylvania State University. Valeria Custadio, David Gopolchan, Dylan Jones, Darren Wells and Gabriel Castrillo of the University of Nottingham. Jesus Salis-González of the Universidad Nacional Autónoma de México; and Angela Moreno of the Ministry of Agriculture and Environment in Cape Verde.
“One of the things that makes this work valuable is how contradictory it was,” Wagner said. “We bring together genetic analysis, plant physiology and microbiology, which allows us to address and answer questions that could not be addressed before.”
This work was funded by the National Science Foundation's Division of Integrative Systems Biology.