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Washington State University

Roots of the matter

R. James Cook and soil health

Soil teems with microorganisms, both harmful and beneficial, waiting for a host. “It’s a jungle in there,” says R. James Cook about the soil around roots. That jungle with its pathogens can cause any number of diseases that will affect one of Washington’s signature crops, wheat.

“Root diseases were a big part of what we needed to deal with in order to achieve the full production capability of wheat growing in our rich Palouse soils, and our rich dry land soils farther to the west,” says Cook, a former researcher with the U.S. Department of Agriculture Agricultural Research Service (USDA‑ARS) at Washington State University.

Over the course of four decades with WSU and the USDA‑ARS, Cook not only tackled the control of those root diseases with fervor, but he established one of best soil health research units in the world.

He garnered numerous prestigious honors—including the 2011 Wolf Prize for outstanding scientific contributions to agriculture, election to the National Academy of Sciences in 1993, president of both the American Phytopathological Society and the International Society for Plant Pathology, and a founding member and past president of the Washington State Academy of Sciences, among others.

Cook received WSU’s highest award, an honorary doctoral degree, on Dec. 8, 2018, in recognition for his long service to the University and to the cause of healthier plants and soil.

“We didn’t call it soil,” says Cook, looking back on his childhood. “We called it dirt.”

Cook grew up on a 400‑acre farm in northwestern Minnesota, just across the border from North Dakota. Born in 1937, he was the oldest of eight kids, and helped out with the chickens, dairy cattle, and crops from the time he was five years old. Cook remembers how they harvested grain with a binder and tied it in bundles, and then put it into a threshing machine, with the threshed straw used as bedding in the barn. One of the happiest days of my life, he says, “was when I graduated to drive the tractor and didn’t have to ride the binder anymore.”

Cook went on to North Dakota Agricultural College (now North Dakota State University) to study agronomy and animal science, planning to become a farmer. But, he points out, agriculture was changing, becoming more concentrated as farms converted entirely to crops or livestock feedlots and huge dairies.

He was dating Beverly Ann Miller at the time and took her out to the family farm. “I’d show her around and she thought the farm was very interesting, but then she announced to me, as we were getting engaged, ‘Well I really like to visit the farm, but I’m not gonna live on a farm,’” says Cook. “And with that, my career took an about face.”

Cook had worked for a plant virologist as an undergraduate, which led to graduate work at North Dakota State. In 1960, he became the first student to get a plant pathology degree there and, masters in hand, Cook went to the University of California Berkeley for his doctorate. It was there that soil really captured his curiosity.

Berkeley in the early 1960s held a hub of scientists working on root diseases and biological control. Since soil‑borne pathogens don’t have a cost‑effective chemical solution, researchers began using the pathogens’ own microbial enemies to manage them on plant roots. Those helpful organisms then live on the roots where they make natural antibiotics or have other processes to provide a defense system against root diseases.

Cook joined that research effort in its infancy, focusing on root diseases of beans and learning from top plant pathologists about biological control. That also led to a fellowship in Adelaide, Australia, after earning his doctorate in 1964.

“Bev and I took our two young children on an ocean liner for 28 days to Australia,” he says. They lived there for 14 months before receiving a job offer at the USDA‑ARS research group in Pullman. Since the Palouse is prime wheat country, Cook recognized the potential for research collaboration on soil health and root diseases, and took the job at Washington State.

In 1965, when Cook joined about 25 other USDA‑ARS scientists at WSU, C. Clement French was president and WSU only had around 15,000 students. Cook moved into his office in Johnson Hall, then just five years old, and set right to work on his mission.

Cook consciously uses the word “mission” to describe the work of USDA‑ARS scientists. They hold appointments with the university, but their work has a defined focus.

“A new faculty member arriving at the university is usually allowed to take off in any direction they want, pursuing their interests and doing curiosity-driven research,” he explains. “I was hired to do a very specific job, which was to understand and control the root diseases of wheat. The man who hired me said, ‘You can study them if you want, but your job is to control them.’”

That didn’t faze Cook. “It might seem like I was put into a box and doing so‑called mission‑linked research, but it’s not like I didn’t have any curiosity going about my job. I’m curious about so many different aspects of the root disease problem on wheat.”

Those root diseases and soil‑borne pathogens, and their control with beneficial organisms, weren’t very well‑known when Cook began his work at Washington State. He had the opportunity to join colleagues across the Pacific Northwest and study root diseases, such as Fusarium root and crown rot of dryland wheat and take‑all in areas with irrigation. Cook and his fellow crop scientists didn’t just focus on Pullman, but expanded their work to Mount Vernon, Puyallup, Lind, other WSU experimental stations, and on different farms.

In one significant example in 1971, a number of bags of diseased wheat roots from Puyallup sat on the table in Cook’s lab. The wheat had suffered from a nasty root fungus called take‑all that left them with blackened roots. Except Cook immediately noticed four bags with healthy white roots.

“Take‑all is caused by a fungus that lives in the roots of the crop just harvested, and grows from those decaying roots onto the fresh roots of the new crop to rot them off and cause wheat to die in big patches,” he says.

A European study in the late 1960s showed that the soil would become suppressive to that very same fungus, if you just kept growing wheat. “Just the opposite of what we would normally do,” notes Cook.

For the experiment, he and his colleagues raised wheat with take‑all, but included some soil from a field near Quincy, Washington, that had wheat growing consistently for 12 years. That was the wheat with healthy white roots, confirming the soil was in take‑all decline.

It “changed the direction of my program completely.”
Cook, reflecting on his take‑all decline finding

The take‑all decline finding “changed the direction of my program completely. That one experiment, done in the field.”

Cook also did some myth‑busting in his work. For 30 years, there was a belief that straw from wheat was toxic to wheat. “I had to deal with that diagnosis and it was well established in the scientific literature, but it was wrong,” he says. He proved through a series of experiments that the problem came from root diseases thriving under the wet blanket of straw on the soil surface.

“I showed that I could fumigate the soil and then bring fresh straw back that had not been fumigated,” says Cook. “There was absolutely no evidence of toxicity once the soil was rendered free of pathogens with fumigation.”

Still, fumigation is not a sustainable solution for root diseases, Cook notes. “We have an array of chemicals that we can use to protect the crop above ground. Soil fumigation is really the only chemical means by which to truly control root diseases, and that’s not going to be economical except for high value horticultural crops like strawberries.”

Cook’s research didn’t just stay in the lab. He cultivated strong relationships with wheat growers all across the region. “I got to know some really great farm families doing research in their backyard, where the problems were, rather than just bringing the problems to the lab at WSU,” he says.

The farmers, in turn, respected Cook and his efforts. “In particular, because of my farm upbringing, and interest in crop science and agronomy, I was very much accepted by the grower community and I loved to have the growers come and see my experiments and be able to share what was happening there. I’d try to provide them with some take‑home information that they could apply on their farm,” says Cook.

“Growers really appreciate good science, especially when it’s happening on their own farm.”

John Aeschliman, who has a farm outside of Colfax, was one of those growers who developed a strong rapport with Cook.

“He grew up as a farm kid and he spoke farm language,” says Aeschliman. “Jim’s ability to communicate was really high, so growers would go to him. Root diseases—Rhizoctonia, Cercosporella, foot rot, take‑all—all these diseases were very prevalent during his time at the university and he went after them with vengeance.”

“Growers really appreciate good science, especially when it’s happening on their own farm.”
Jim Cook

Cook also connected with legendary Washington State wheat breeder Orville Vogel, who developed a great deal of respect for Cook’s research on root diseases and soil-borne pathogen. Early in his time at WSU, Cook demonstrated to Vogel that soil pathogens were limiting the yields on semi‑dwarf varieties like the famous variety Gaines. Vogel’s response to the fumigated plots: “That’s how my wheat is supposed to look!”

“Orville was a great mentor and friend” says Cook. “He used to come to my office and say, ‘Come on, let’s go out and look at some wheat.’ He carried a little trowel with him, and he’d dig up some plants and ask, ‘Now, what’s this?’”

Cook himself served as a guide for many researchers and graduate students who came to both WSU and the USDA‑ARS. David Weller and Linda Thomashow were two scientists who joined Cook in researching root diseases like take‑all and take-all suppressive soils at the university.

“Jim was an incredible mentor,” says Weller. “And his work on biological control was groundbreaking.”

Weller, who now works in Cook’s old Johnson Hall office, reaches up and pulls two well‑used hardbound books from the shelf. “I still use these two books that Jim co‑wrote on biological control. He has such an encyclopedic mind, and taught so much to us.”

Weller had met Cook as a young doctoral student at Michigan State in 1978, where Cook was a guest presenter. He asked Weller if he’d like to help with a grant he had at WSU, studying take‑all decline. “My wife and I moved to Pullman, thinking we’d be here for a couple of years,” says Weller. “We’ve been here for forty.”

Cook’s influence extended to visiting scientists and a number of graduate students from Thailand, Brazil, Japan, England, and across the United States. Deb Inglis (‘78 MS, ‘82 PhD) benefited from Cook’s guidance as a graduate student.

Inglis was a farm girl herself near Spokane and knew Cook’s reputation. “My grandfathers needed answers to real life problems, since they both grew cereal crops. Jim, of course, worked on root diseases of cereals and he worked very closely with farmers. I really wanted to work with someone who could relate to farmers and who could help answer real life issues and problems,” she says.

She says Cook’s ability to be theoretical and practical at the same time came through to his graduate students. “One thing he always told us as graduate students, when you think applied research you need to do fundamental research, and think fundamental when you do applied research. And that motto has served me well in my career.”

Inglis later became director of the WSU Mount Vernon Research Center where she applied Cook’s teaching. “I think hypothesis-driven research that is field based, observations that one sees in the field, and then solutions that are attempted to be found through laboratory, greenhouse, and sometimes field research, that’s a winning combination,” she says.

Just east of the WSU Pullman campus, 160 acres of farmland, now called the R.J. Cook Agronomy Farm, continues Cook’s soil research and fulfills his vision of a research site into issues like soil loss. It was selected in 2011 as a USDA Long‑Term Agroecological Research site, under the stewardship of soil scientist David Huggins. It began 11 years before as a place for Cook and his colleagues to test in a realistic setting.

“Growers knew I did field research, but they said, ‘We want you to do research on a scale we can relate to, no more of those little plots,’” says Cook.

“We had a motto that we want to do world class farming and world class science at the same time,” says Cook. “And let the neighbors, as they drive down the county road, look at the fields and see how we’re doing.”

That farm also featured another area of Cook’s interest since the 1980s: direct seed, also called no‑till farming. Although it wasn’t widely accepted at the time, direct seed methods use a drill to plant seeds and place fertilizer with minimal disturbance from tillage, thus reducing the risk of soil erosion. Cook saw that erosion could affect even his work on root diseases.

“If I continued to do research on how to control the root diseases in conventionally prepared seed beds and then that becomes obsolete, I better be working on no‑till now and not wait until the conversion has taken place in the industry,” says Cook.

He saw no‑till as financial win for farmers as well. “It was more economical to be able to farm with a sprayer, a combine, and a harvester as opposed to all the tillage equipment, which they could park out in the back forty and let it rust in peace.”

Aeschliman was an early adopter of no-till in the mid‑1980s who worked with Cook, recognizing the savings in “soil, toil, and oil” from direct seeding.

The reality of soil erosion also encouraged Aeschliman to work with Cook on no‑till. “Our biggest problem here in Whitman County is soil erosion, soil leaving the fields,” says Aeschliman. “It’s your fertilizer going into the ditch.”

The precision agriculture work at the Cook Agronomy Farm has now evolved into broader work on efficient and resilient use of farmland resources like water and soil.

After he retired in 2005, Cook heard the news that they named the farm after him. “I knew then that my mark was going to be on that farm into perpetuity,” he says, “So I’ve continued to watch what’s happening there and see all younger scientists find a place to do their research.”

Cook’s direct impacts on crop productivity and disease management were also recognized in 1998 by Washington wheat growers with a $1.5 million endowment to establish the R. James Cook Endowed Chair in Wheat Research. Cook became a full‑time WSU faculty member that year and served in his namesake endowed chair until 2003.

In 2003, WSU President V. Lane Rawlins asked Cook to serve as interim dean of the College of Agricultural, Human, and Natural Resources Sciences during his final two years at WSU, which Cook accepted until his retirement in 2005 as an emeritus professor. Jim and Bev Cook now split their time between Bothell as their official residence, their home on Lake Coeur d’Alene in the summer, winters in Palm Springs, California, as snowbirds.

One is more likely to find a grapefruit than a stalk of wheat in Palm Springs, but Cook remains connected to WSU and his research interests. In his retirement, Cook continues to present at conferences, assist with National Academy of Sciences outreach, and, along with Beverly, help lead the “Cougars of the Desert” group in Palm Desert near their home, which raises money for WSU scholarships.

Cook’s legacy, now recognized in 2018 by Washington State University with an honorary doctoral degree, is one of leadership in conservation-oriented agriculture, research acumen, and decades of service to farmers and the agricultural community.

As Scot Hulbert, chair of the plant pathology department at WSU and the R.J. Cook Chair for Cropping Systems Pathology, sums it up: “His exceptional contributions in plant and microbial biology established WSU as a leader in the area of soil microbes as beneficial components of cropping systems. He popularized research in soil microbial communities long before ‘microbiome’ research became popular.”

“The contributions he has made have really changed how wheat and other cereal grains are growing in our state and our region.”
Inglis, on Cook’s contributions to the WSU program

Inglis says it’s hard to imagine the WSU program without Cook’s contributions. “Root diseases, water relations, biological control, tillage practices, fertility and water management practices, breeding for resistance, he’s had his hand in all of those areas,” she says. “And the contributions he has made have really changed how wheat and other cereal grains are growing in our state and our region.”

She also points out how Cook connected so well with farmers and the entire agricultural community. “He could relate to them on their level, but he also has a wonderful way of explaining fairly complex phenomena in ways that people can understand,” says Inglis. “I remember him talking about the jungle of roots beneath the soil, just using metaphors and explanations that people could easily relate to and really acquire his enthusiasm.”

Although he held many honors and conducted significant research, Cook never forgot his service to the farmers, always keeping one foot in the lab and another in the field.

“I avoided telling farmers what to do, but rather, set about providing them with enough understanding so they would know what to do,” wrote Cook in his 2017 memoir, Untold Stories: Forty Years of Research on Root Diseases of Wheat.

Through it all, Cook was most proud that research colleagues and farmers saw him as having “two feet in the furrow,” which allowed him to accomplish his mission, communicate his work, and still satisfy his deep curiosity about root diseases and the jungle of soil life.