Plants require strong roots and good soil to thrive and produce a bountiful crop, but that is a challenge when soil is affected by drought, low nutrients or salinity.
Daniel Schachtman, a University of Nebraska–Lincoln professor of agronomy and horticulture, studies how root systems and soils affect plant growth, disease resistance and crop yields and ultimately, how crops can grow in poor soils and drought conditions.
UNDERSTANDING MICROBES, IMPROVING GROWING POTENTIAL
Schachtman’s research is conducted in hopes of finding an ideal group of microbes that will help plants grow in stressful environments. His focus is in understanding the microbes– bacteria or fungus– that interact inside and outside of the plant root. He is learning how the environment affects the community of root microbes, called the root microbiome, and how that community impacts the plants. Schachtman and scientists with whom he collaborates collect data on roots’ environmental stresses, including low nitrogen, salinity, drought and water deficit. Some of his research studies root exudates, which are compounds the root releases into the soil on which microbes feed and grow. Exudates include hormones, amino acid, organic acids and sugars that are released by plant roots and act as a source of nutrients for the microbes, Schachtman said. He hopes eventually to engineer the plants so they can grow in low-water, low-nitrogen conditions or in soils that are experiencing drought, with the assistance of specialized microbes.
If Schachtman and his collaborators are successful, it is possible that farmers could use less fertilizer in their fields, reducing their costs, keeping yields high and reducing groundwater pollution, he said. For example, the nitrogen from plants in sandier soils in Nebraska leaches into the water table, eventually making its way downstream and polluting waterways. Schachtman’s research currently is in the process of finding microbes that would help plants make their own nitrogen to solve this problem.
“Microbes are cool. They can be applied to agriculture but there are all sorts of industrial uses for microbes also,” Schachtman said. Microbes are useful in many different ways, from making yogurt to making ethanol, he added.
Another large research project involves the university’s Center for Root and Rhizobiome Innovation that engages researchers from the University of Nebraska–Lincoln, the University of Nebraska at Kearney, Doane University and the University of Nebraska Medical Center. Schachtman said researchers are screening 400 lines of maize and will conduct detailed studies on 30 lines that have very different exudate profiles. They will be planted, then scientists will measure how the microbial communities change across the different lines depending on exudates. The Center for Root and Rhizobiome Innovation was established and funded by the National Science Foundation Experimental Program to Stimulate Competitive Research (EPSCoR) program. His work as part of this project focuses on maize and on differences in exudates, but the research will transfer to other crops.
Schachtman said yet another research project focuses on sorghum and growing high biomass yielding plants on marginal land for making cellulosic ethanol– this marginal land might be low in nitrogen or might not get enough water.
“We are using sorghum as the plant we are studying, and we are screening lines for drought tolerance and nitrogen deficiency,” Schachtman said. “We hope to find an ideal group of microbes that will aid plants that are growing in these low-nitrogen, low-water or droughted soils.”
Schachtman started his research in 2014, when he joined the university faculty, by sampling fields and water in many Nebraska locations, looking at how nitrogen and drought alter microbial communities. Through the research processes, large amounts of data are collected about the microbes.
“These data sets are huge,” Schachtman said. “There are special open-access programs available for handling all of the (DNA) sequencing data, checking the quality and getting it into a form we can analyze, and some programs that allow us to do a basic analysis,” he explained. However, it takes specific expertise to analyze large amounts of complex data– a combination of knowledge of both biology and statistics, called bioinformatics. Schachtman’s laboratory includes post-doctoral researchers, graduate students and technicians who are involved in analyzing and making sense of the data using a graphical representation of the data and statistical methods to test for differences in treatments and in genotypes– always in the microbial communities.
Through this data collection, Schachtman is able to learn what microbes have the potential to provide high yields, nitrogen and drought resistance. The vision for this research is to lower costs, increase profit potential for farmers and protect our natural resources.
CENTER FOR BIOTECHNOLOGY
Schachtman also is director of the university’s Center for Biotechnology. Founded in 1987, the center provides faculty, staff and students with access to state-of-the-art instrumentation and experts in multiple areas of research. The center has grown to include five core facilities: bioinformatics; flow cytometry; microscopy; plant transformation; and proteomics and metabolomics, each led by an expert in that discipline. Each core facility houses scientific instruments that can each cost up to a million dollars; the core facilities eliminate the need for multiple laboratories to purchase their own equipment by offering fee-based services and training to faculty, students and staff.
“Plant scientists bring in plants; people studying animals bring in tissue culture samples; people interested in microbes will bring in bacterial or fungal samples; engineers bring in fabricated materials, biological engineers will bring in tissue samples,” he said. As an example, one company is interested in assuring the purity of its vaccines, so the Center for Biotechnology experts examine the vaccines for viral particles to be sure they are clean, he explained.
The Center for Biotechnology scientists also conduct periodic training sessions and a course for students in which they learn about each core facility.
“Our goal is to serve our customers, process the samples quickly and provide the instrumentation so faculty have the tools they need for their research,” he said.
