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UW professor uncovers microbes that could replace fertilizers

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UW microbiology and environmental science professor Sharon Doty’s groundbreaking research could help reduce carbon emissions from agriculture. It turns out that certain microbes can help life grow in nitrogen-poor environments, and these microbes might eventually be able to replace fossil fuel-guzzling fertilizers. 

“During my postdoctoral research in the UW biochemistry department, I was doing poplar tree tissue culture,” Doty said. “When I would cut open the surface-sterilized poplar stems, I would often see a prolific, slimy growth. I decided to identify it so maybe I could kill it better since I thought it was interfering with my experiment. I was astonished to discover that it was Rhizobium, a well-known microbe associated with legumes where it fixes nitrogen in root nodules.” 

Her lab went on to demonstrate that these microbes inside of the trees can “fix” nitrogen, meaning that they take atmospheric nitrogen that plants are unable to use and convert it into a usable form. In other words, the microbes allow plants to grow naturally in places where normally they would require nitrogen fertilizers.

Doty and her team wanted to know if the microbes could help with sustainable agriculture. When her lab injected the microbes into crops like tomatoes and peppers, as well as popular commercial trees such as the Douglas Fir, the results were promising. 

“The plants given the microbes of wild poplar and its relative, willow, were able to outperform the uninoculated plants in low nutrient soil,” Doty said. “Not only do the microbes improve plant growth, they also helped the plants be more drought tolerant, a hugely important trait these days. My lab has also shown that specific bacteria can degrade environmental pollutants and fight off fungal pathogens. So the plant microbiome can have profound impacts on agriculture, forestry, and environmental restoration.” 

Doty’s lab has experimented widely with endophytes, which are bacteria or yeast that inhabit plant cells. Nearly every plant on earth serves as a host to one or more endophytes. When first discovered, it was believed that these organisms were parasites, but over many decades it became clear that quite the opposite was true. They benefit their host plants dramatically.

“Like many people, I thought of bacteria as primarily pathogenic organisms, and I didn’t know much about the plant microbiome,” Robert Tournay, a graduate student under Doty, said. “I found the idea that plants are internally colonized by beneficial microbes interesting, and thought that Dr. Doty’s work on how these mutualistic microbes help their host plants tolerate different environmental stresses to be a very exciting area of research.” 

Besides fixing nitrogen, endophytes prevent other bacteria or fungi from colonizing their host plant by competitively excluding them. In return, they receive carbon as food from the plant. They can also produce secondary metabolites, chemicals that are toxic to herbivores and prevent the plants from becoming an afternoon snack for an unsuspecting deer. 

“I think what is interesting is how intimate the relationship is between plants and their microbiome,” Tournay said. “Nitrogen-fixation is only a single example of how endophytes may make their host plants more tolerant to environmental stresses. There is evidence that endophytes can help their host plants in many ways, such as the acquisition of essential nutrients besides nitrogen, inhibition of pathogens, and increased tolerance to drought or high saline soils. Additionally, we are investigating whether endophytes might make plants more efficient at phytoremediation of different environmental pollutants.”

Doty received her Bachelor of Science in genetics from the University of California in 1989, and went on to receive her Ph.D. in microbiology from the UW in 1995. Her lab is focused primarily on the symbiotic relationship between endophytes, which are bacteria and fungi that live inside of plants, and how this relationship might benefit agriculture, forestry, and biofuel production.

If you’ve spent any time on a farm or in a garden, perhaps you’ve heard just how important nitrogen is to the health of plants. But plants are just plants, right? How could they possibly be so sensitive to delicate nutrient balances? 

It stems from the fact that plants are life forms, and like all life, including humans, they need nitrogen. Nitrogen is used to build DNA, among many other things. It’s the reason that nitrogen fertilizers are dumped by the millions of tons on crops each year. This is good news for us, as it enables us to maximize our crop yields and produce an opulent abundance of crops. However, these fertilizers spell bad news for the ecosystem.

“Chemical fertilizer production is an energy-intensive process using fossil fuels,” Doty said. “They are then applied in excess in agriculture since it would be too costly to administer them frequently at the low rates at which the plants can take them up.  What is left in the soil can be converted by soil microbes to nitrous oxide, a potent greenhouse gas.” 

That’s not all. These fertilizers have a tendency to appear in streams, rivers, and lakes, eventually winding up in larger bodies of water. There, they create dead zones, which are areas in the water where life cannot exist.

“The excess also leaches into aquatic systems where it disrupts those ecosystems, often resulting in algal blooms that deplete oxygen levels and kill fish.” Doty said. 

There are roughly 400 dead zones globally, and each can span many thousands of square miles. These dead zones cost the fishing industry millions of dollars every year. Clearly, current levels of fertilizer use are unsustainable in the long run, but “people gotta eat” just as much as “fish gotta swim.” Profitable alternatives must be unearthed if we ever hope to stymie the degradation of our environment. Doty’s research suggests that endophytes could eventually become one of those alternatives.

Many aspects of these bizarre microbes still remain poorly understood, however. It’s these details that Doty’s lab is helping tease out. Just how do endophytes interact with plants, and how can the benefits of the endophytes eventually loosen our society’s dependence on fertilizers?

But Doty’s lab is looking even further ahead. 

“A couple of our endophytes are the first to go in space,” Doty said. “They are currently on the International Space Station. Ultimately when we colonize mars and the moon, we would like to use plant microbes to help the crop plants grow in that ‘soil.’”  

To learn more about about the fascinating work that Dr. Doty and her students are working on, visit her website


Reach writer Tony Scigliano at Twitter: @earthtotones









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