Researchers to improve nitrogen-fixing capabilities in soybeans

A new project from South Dakota State University's College of Natural Sciences looks to improve the soybean plant's ability to naturally fix nitrogen, reducing the need for synthetic fertilizers.\

Soybeans are the world's fourth-most grown crop and are used for foods like tofu and soy-based products but are primarily grown for animal feed. In South Dakota, the 223,080,000 bushels grown in 2023 were valued at over $2.76 billion, per the U.S. Department of Agriculture.

USDA projections show the global trade of soybeans is likely to increase by as much as 22% in the coming years. The increased demand is fueled primarily by growing populations in the Global South and the widespread use of biodiesel, which is made from soybean oil.

In short, soybeans are big business, especially in South Dakota, and their value is projected to increase.

As the need for soybeans increases, South Dakota State University researchers are looking at ways to improve the crop's value and productivity for farmers in the region.

Soybeans and nitrogen

One of the reasons soybeans have become a multibillion-dollar industry and a staple in crop rotations throughout the U.S. is the plant's ability to take nitrogen from the atmosphere, fix it in the plant's root structures — these are known as "nodules" — with the help of bacteria and then use it as a nutrient. This cuts down on input costs and also reduces the management needs of the crop.

But for some high yield varieties, when the soybean plant reaches later growth stages, they are unable to supply the necessary amount of nitrogen — an essential nutrient — due to the accumulation of storage proteins in seeds. To offset this, farmers apply environmentally harmful and energy-intensive synthetic fertilizers to ensure the crop is meeting its nitrogen needs. Soybeans will also deplete the soil of its precious nitrogen as it continues to grow, causing soil problems for farmers in later years.

SDSU College of Natural Science researchers Senthil Subramanian and Bhanu Petla believe they may have a solution. They hypothesize that by delaying the maturity of root nodules in soybean plants, the natural process of biological nitrogen fixation could continue to meet the plant's nutrient needs later in the growth cycle. This would ensure yields remain high without the application of synthetic fertilizers. 

"In high yielding soybean varieties, nitrogen supplied by nitrogen fixation is not sufficient to meet the needs of plant during reproductive stages," Petla explained. "Plants need to take up nitrogen either from soil or supplied through fertilizers, which results in poor soil health and high input costs. We would like to address this by delaying nodule maturation to supply nitrogen through reproductive stages."

"We expect to find, or generate through genome editing, soybeans with higher nitrogen fixing capacity," Subramanian said. "The ability of SDSU post-doctoral associates to serve as co-primary investigators on grant proposals greatly helped Dr. Petla’s professional development. Preliminary data for this project came from an NSF-EPSCoR and a Research Experience for Undergraduates (REU) research project of SDSU undergraduate Marissa Dreissen."

According to past research, biological nitrogen fixation provides, at most, 60% of the plant's nitrogen needs. The key to biological nitrogen fixation is in the roots of soybeans. As the plant grows, so does its nodules — small, ball-like structures that are found in the roots and form a symbiosis with nitrogen-fixing bacteria, which helps provide the plant with its nitrogen needs. The number of nodules per soybean plant, research has shown, is a critical component to crop yield. The more nodules, the more nitrogen that can be supplied, which leads to larger yields and, in turn, more value for farmers.

"We hypothesize that soybean genotypes with a higher number of nodules with delayed maturation can fix nitrogen in the reproductive stages and help meet nitrogen needs in a sustainable manner," Petla said.

The Subramanian Lab has shown in previous research that different levels of two different types of growth hormones, auxin and cytokinin, promote nodule formation and delay maturation. The researchers believe that genetic variations in soybean cultivars leading to reduced levels of auxin but higher levels of cytokinin can result in a higher number of nodules with delayed maturity. This would allow for biological nitrogen fixation to meet the plant's nitrogen needs later in the growth cycle, thus reducing — or even eliminating — the need for costly synthetic fertilizers.

To find the desired traits, the researchers will genetically edit the genome sequences of the soybean plant with CRISPR — an advanced gene-editing technology. Specifically, they will be looking at precisely what hormone genes are responsible for nodule numbers, delayed nodule maturity and aging in soybeans. This will require testing over 1,000 different genomes. Once the researchers have identified the desired genetic variants, they will work with soybean breeders to incorporate these traits into elite, high-yield soybean cultivars.

"This seed grant project will evaluate natural genetic variation available in soybean germplasm in auxin and cytokinin biosynthesis pathway genes and evaluate their nodulation and nitrogen fixation capacities," Petla said.

The project will work in three phases and will greatly contribute to understanding the role hormone responses have in regard to root nodule development and soybean growth.

"This project will help us identify natural variation in delayed nodule maturation during reproductive stages," Petla said. "In the future, transferring this trait to elite varieties will improve yield and reduce plant demand for nitrogen from soil."

This two-year, $300,000 project, titled "Evaluation of natural and genome-edited genetic variations in auxin and cytokinin pathway genes for optimal nitrogen fixation in soybean," is being funded through a grant from the USDA's National Institute of Food and Agriculture.