Interview: Endophyte Innovations

John Kempf. One of the things I’ve come to really appreciate is how much valuable historical knowledge has been lost or has been ignored. When we look back at the domain of understanding disease-suppressive soils and understanding soil microbiology, there’s research going back all the way to the early 1900s postulating plant absorption of nutrients through a process called endocytosis. There’s research describing all of the potential impacts that soil biology can have on plant development. But for many years, a lot of that research was ignored. We prioritized chemistry rather than biology.

And recently, with the work of Drs. James White and David Johnson and Christine Jones, and many other pioneers in this space, we’ve come to appreciate the critical importance of the role of biology in living systems. Fundamentally, regenerative agriculture is about understanding, facilitating and regenerating these relationships — between livestock on the landscape or between plants and soil microbes. 

Mary, you’re another one of these pioneering scientists who first discovered some of these important relationships between microbes and plants. Why don’t you tell us a bit about your personal story and the research you started working on decades ago? 

Mary Lucero. Thank you, John. Well, I’m a 16th-generation New Mexican. My family history goes back as far as there is recorded history in New Mexico, and probably further. And because of that, there’s this tie to the environment and to the land that is maybe less on the forefront of the minds of people who have not been in the same place as long. 

My degree was in molecular biology. I was very much in a biotech environment, and my goal was to apply this to environmental restoration. For family reasons, I stayed in New Mexico to do that; there really wasn’t a degree program that focused on environmental applications of molecular biology, so I was interacting all the time with the plant molecular biologists who were doing genetic engineering for agricultural purposes. In fact, there was a big effort to develop and genetically engineer green chili at the time, because that’s one of the biggest crops in the state.

I went to graduate school thinking I was going to engineer microbes to break down chemical waste. But I’d only been there a few months before the consensus had been reached among the scientists that this really wasn’t a practical approach. Because when you take a microbe out of the environment and culture it long enough to engineer it, it has lost all the genes that give it the ability to function in the environment. When you put it back out there, it’s really not cleaning up much of anything. It’s getting eaten — it becomes food for other microbes. 

So, the effort in microbial ecology at that point was to create the environment that allows native microbes to thrive. Do you change the nutrients in the soil? Do you change the aeration? What do you have to do to create that environment, because microbes are already there — they just need the right food to get them going. 

Now, my undergraduate work was in agriculture, and I married into a family that was ranching at the time, so there was all this agricultural influence; it just wasn’t a good time to get into agriculture. That was probably what motivated my interest in environmental science. 

My doctoral research focused on using what was the new horizon at the time — the plant-microbe interface. We were looking at using plant and microbe communities to break down environmental waste. We actually found a plant — common jimsonweed, Datura — that could chew up TNT faster than any microbe that had ever been tested. In New Mexico, during World War II, there was a lot of weapons testing, and as they were developing the atomic bomb, they manufactured a lot of TNT. Our research was working very well and going very quickly. 

And the question came up, is it really the plant that’s breaking down the TNT, or is it microbes associated with the plant? At the time, the perception was that if you grew a plant in micropropagation — in tissue culture — you were dealing with an axenic system — one in which there were no microbes associated with it. So, we decided to grow the plants in tissue culture, feed them TNT, and see if they could break it down. And yes, it broke the TNT down very quickly. 

About three weeks before I defended my dissertation, though, I was cleaning up my cell cultures in the lab, and I had done a final contamination check to make sure there were no microbes growing on the plant, and everything came out clean. I said something like, “Yay, now I can defend!” But one of the technicians who was working in the lab with me kind of chuckled. He said, “Before you decide that those plants are axenic, you might want to go talk to Jerry Barrow.”

I looked at him and said, “Who’s Jerry Barrow?” and he said, “He’s some old USDA guy who thinks that all plants are high-order lichens.” I’m the kind of personality who, when I hear something really out of the box, I need to go listen and get the whole story. And so about two days later, I’m knocking on the door of Jerry Barrow’s office. He invited me in to chat about microbes, and he started showing me micrographs he had taken of what he claimed were fungal structures inside micro-propagated plant tissues. He was working in a range ecology unit in Las Cruces, at a large USDA Ag Research Service facility. He was looking at how microbes were influencing the advancement of woody shrubs. He had hundreds of images of stained cells of fungal cell walls and fungal lipids inside the plant. He had thousands of these microbe graphs showing fungal structures in every single tissue of the plant.

And I remember looking at this picture, getting goosebumps, thinking, “If this man’s data are correct, pretty much everything I’ve learned in plant biotechnology is skewed.”

But the weakness to Jerry’s work at the time was that you need to look at things with many kinds of data, and all he really had was microscopy and many failed efforts to isolate these microbes from the plant in tissue culture. The problem was that he was looking at endophytes that, by nature, are optimized to live inside the plant. We know that 98 percent of the microbes in the environment can’t be cultured on plates. He was getting very inconsistent results trying to separate these microbes from the plant. And so, of course, I jumped in. I was finishing my dissertation and needed a job, so I said, “I can do the DNA sequencing, and let’s prove that they’re there.” 

Well, it took us a few years to work in the funding and to create that position and to build on that opportunity. I actually spent about 10 years with USDA, working very closely with Jerry Barrow and others to isolate these endophytes from black grama grass and from fourwing saltbush — those were the two model systems we were looking at. We ended up characterizing many endophytes that lived in the plant while it was in so-called axenic environments — while it was in cultures that did appear to be axenic, by common standards. We published papers on these microbial communities that lived inside these plants.