The Evolution of Discovery

How the engine of research spurs the endless pursuit of understanding

By Heidi Happonen

S

ometimes scientific research can feel like laundry. It’s never really done. The goalpost is always moving as new discoveries reveal new questions which in turn inspire new research. However, unlike laundry, scientific research isn’t an endless repeating cycle of sameness. It’s an iterative, compounding process that advances progress and understanding.

Research is discovery.

The pages of this magazine often detail the impact of a particular research project and its role in shaping fundamental changes in how we understand and adapt to demands on our agricultural and natural resource systems. But what is equally as fascinating is how this research even begins—where does the idea form and how does it grow from a problem identified in the field to a solution formulated in a lab (which also is often a literal field).

This is the story of that process through the lens of one research group’s pursuit to find a new way to combat plant disease. And as a land-grant institution, it is also the story of how interconnected our research mission is to both outreach and education. 

Outreach. Out There.

Let’s start with outreach—often the starting point of research where diverse stakeholders share their challenges and come to the College of Agricultural Sciences seeking solutions.

With 14 experiment station locations across the state and embedded research collaborations with institutions across the nation around the world, our scientists are constantly responding to some of the most pressing challenges facing our agriculture and natural resource systems. It is in listening to these challenges where the seeds of meaningful questions are formed which in turn lead to defined research projects that seek to answer those questions.

Posy Busby examines how variation in leaf wax influences microbial community composition and pathogen antagonism in a cottonwood common garden experiment.

One constant, ever-evolving challenge in agriculture is plant disease. According to the National Institutes of Health (NIH), plant pathogens and pests are responsible for up to 40% of maize, potato, rice, soybean, and wheat crop yield losses worldwide. Further, one of the most devastating pathogens, R.solanacearum is responsible for an estimated $1 billion in losses each year– just for potatoes.  In total, each year plant diseases cost the global economy around $220 billion.

Combatting plant disease in particular presents cascading challenges in a war where these diseases are constantly evolving to gain resistance to our latest efforts to defeat them. So, the question emerges….

What if, instead of perpetually fighting this battle with new external weapons (pesticides, herbicides, and other human-made barriers), we harnessed the innate power of the plant itself to fight off disease by recruiting naturally occurring, beneficial microbial partners from the environment.   

From a Question to the Pursuit of an Answer

Populus trichocarpa, the black cottonwood native to the Pacific Northwest.

Fundamentally, scientific research is the methodological discipline for finding answers to “what if” questions. This particular “what if” question about harnessing the power of naturally occurring microbial systems to combat plant disease falls under a number of diverse scientific disciplines: plant pathology and breeding, biology, soil science, and more. Those disciplines are united under a program established in 2016 by the National Science Foundation (NSF): Understanding the Rules of Life (URoL). The goal of this program when it was launched was to “identify generalizable rules that govern biological systems at micro and macro levels.”

Seven years later, this program is still going strong with newly refined focus each year. One of the leading scientists active in the pursuit of this “what if” question and engaged with this highly-competitive NSF program is Posy Busby, an Associate Professor in the College’s Botany and Plant Pathology department.

As is the case in all scientific discovery, the framework and process of research has evolved with new discoveries. According to Busby, the focus of national research in this space has shifted from trying to understand how biological systems at the microbial level work, to intentionally using those systems to improve outcomes in crop and plant production.

In response to that shift, NSF recently updated the name of their program accordingly from Understanding the Rules of Life to Using the Rules of Life. 

Last August, this recently renamed program awarded $27M in new funding to 12 projects led by scientists at institutions around the nation to advance our understanding of this still-emerging area of science. Busby was one of those scientists. 

Combatting plant disease in particular presents cascading challenges in a war where these diseases are constantly evolving to gain resistance to our latest efforts to defeat them.

Two million dollars ($300k of which will be focused on collaborative work at Purdue) was awarded Busby and her team to explore “microbiome-mediated plant genetic resistance” – in other words, breeding crops that are capable of assembling a disease-suppressive microbiome on their own.

Busby and other researchers will build upon past research to further ways to use what nature is already doing to battle disease. Instead of trying to exclude all microbes, including important bacteria and fungi vital to the self-defense of both plant and animal life, they will seek to maximize their benefits. 

Critical funding like this is highly competitive. It is awarded on far more than a “good idea” or even a well-crafted proposal. It is built upon years of proven accomplishments, tireless focus, and collaborative inquisition that advances discovery and points to meaningful progress.

The Pursuit of Funding: Transforming a Good Idea Into Good Science.

Nationally funded research like the kind Busby and her collaborators are pursuing is no accident. It isn’t formed in a vacuum. It evolves over many years of incremental and deliberate progress.

Busby’s latest NSF funding initially evolved from a research incubator program at the College called Ignite. These are internally funded pilot research programs that encourage multi-disciplinary, visionary projects. They encourage faculty to present “big idea” research projects to a review board who in turn select winning submissions for seed funding, often in the neighborhood of $50,000 annually.

Busby applied for Ignite funding in 2019 with her colleague, Chris Mundt, a renowned professor in the Department of Botany and Plant Pathology whose nearly 40 years at Oregon State has left an indelible impact on combatting stripe rust disease for Oregon wheat farmers.

Busby tests how non-pathogenic leaf microbes impact plant physiology using a handheld Licor.

“Chris and I had been talking about collaborating for years, but there just hadn’t been an opportunity,” Busby said. “We had wanted to understand how plants recruit beneficial microbes from the soil and air for some time. The Ignite program was our impetus.”

Mundt added that at the time both he and Busby were busy but independently had fallen onto this idea that they could change the genetics of the plant to alter the microbiome to feed back to the plant.

They theorized that if they could identify plant genes underlying the recruitment of beneficial microbiomes, these genetic regions could become targets in breeding programs. For example, plant genes involved in the production of root exudates (organic carbon compounds, such as sugars, released from living plant roots into the soil) can impact disease-suppressive microbes in the soil. And plant genes that influence the size and number of pores on the leaf surface – a common entry point into the plant – can regulate beneficial microbes that live in and on the leaf surface. 

So “what if” we could harness this already known value at the microbial level to intentionally combat disease?

It was a big idea. A big idea that required resources if Busby and Mundt were ever to put it to the test. And while the Ignite funding is relatively small, it is aptly named to serve as a spark to “ignite” the opportunity to explore big ideas just like this.

“To be honest, I was a bit skeptical at the time about the impact of the Ignite program,” Mundt added. “But it has proven to be a great opportunity for researchers to find ways to collaborate.”

With Ignite funding, Busby and Mundt began recruiting collaborators with expertise across different crops and plants – from hops to hazelnuts. Over the years, that initial seed funding helped spur new research paths and new collaborations.

Graduate student Carolina Pina Paez collecting black cottonwood leaves to evaluate the impact of inoculation with fungal leaf endophytes.

Last year, Busby and Mundt hosted a symposium that was attended by over 60 OSU participants and included outside speakers from Purdue University, UC Davis and Michigan State University. That group has continued with regular monthly meetings that include participants from multiple experiment stations across the state and several departments within the college.

The initial Ignite research awarded $100,000 over two years during which time a core group of researchers collected preliminary data in wheat, tomato, and black cottonwood. They then used that investment to bolster their case to the National Science Foundation for new, larger research under its Rules of Life program

“This all goes back to work I had been doing on cottonwood in my lab,” Busby added.  That research has focused on understanding the rules that govern relationships among plant genotype, beneficial microbes, and pathogenic microbes that in turn has informed the research we are doing today.”

For those not conversant in the differences between genotypes and phenotypes, the genotype refers to the specific set of genes an organism carries in its DNA. For us humans, it represents the inherited genetic information from our birth parents.

Phenotype, on the other hand, refers to the observable characteristics or traits of an organism. These traits can include physical features, behaviors, and other observable attributes.

A parallel effort in the Busby lab explores the assembly and function of fungal communities that associate with Douglas fir needles and roots.

In essence, genotype is the genetic code, while phenotype is the physical expression of that genetic code. The nearly invisible directive that determines the color of your eyes over the physical proof that shows up when you open your eyes and they turn out to be blue (or brown, or both).

Busby’s initial research aimed to uncover how leaf traits under genetic control influence the leaf microbiome. And, in turn, how the leaf microbiome impacts critical plant functions like disease resistance and drought tolerance. Using the Rules of Life, Busby and others sought to figure out the plant genes underlying the recruitment of beneficial microbiomes.

“We were seeking to apply basic biology to take a new approach to sustainable agriculture,” Busby explained. “If we can better understand the factors that control microbial community assembly, then we can get closer to managing plant-microbiome interactions for desired outcomes. We are really looking to add another tool to the toolbox for managing crop health.”

As Busby and her team explored the development of these new tools, an increasingly transdisciplinary approach with an expanded team of experts began to engage with their research.

Big Questions. Big Teams.

In order to effectively approach such a complex challenge, many disciplines and perspectives must join forces. Not only because of the diversity of thought each scientific discipline brings, but in many ways because of the sometimes-surprising commonalities that can be found across species, conditions and geographies.

Mundt, who has pioneered research exploring long-distance disease dispersal, deeply values the opportunity and insight collaborative science can bring to complex problems.

“From stripe-rust disease here, to the West Nile in Kansas to Sudden Oak Death, and Powdery Mildew to Foot and Mouth disease in livestock — there’s an incredible amount we can learn across geographic areas and diseases even between plants and animals,” Mundt explained.

The collaborative nature of this latest NSF funding, as well as the initial college Ignite program seed money, is increasingly becoming the means by which meaningful research is realized.

Leaves of black cottonwood – right leaf colonized by microscopic mites that parasitize plant cells, left leaf uncolonized by the mite.

According to Mundt, there is much more collaboration now in science than there used to be.

“That collaboration is critical,” he added. “When you try to think across disciplines, it’s a tough game, because you can get your interest so broad that you lose depth, but you don’t want to get so narrow that you lose the big picture. So collaborative teams really help to recognize discoveries we can’t find on our own. Biology will always be more complex than we realize.”

Another key player in the growing team of plant microbiome collaborators is  Jim Myers, an Endowed Professor in OSU’s horticulture department. Jim was recruited as part of the research program’s strategic initiative and he in turn brought in Lori Hoagland from Purdue University. Together, they were able to expand application of this research across poplar, wheat and tomato plants in which only further deepens the knowledge and impact of the team’s collective results.

Ultimately, this collaborative approach to scientific discovery creates a community of researchers in the College and beyond who are interested in working on complex problems – in this case, plant microbiomes and how they can enhance sustainable crop production through naturally occurring disease resistance.

As Research Grows, So Grows Teaching.

Part of the growing field of research that Busby and others are leading in understanding plant microbiomes across multiple scientific disciplines and geographies has also led to new opportunities for budding scientists – including both undergraduate and graduate students. Working on emerging science is a huge opportunity for students to gain hands-on experience as they build upon their own growing interest in research.

In 2022, Busby was recognized with a CAREER award from NSF and USDA for her efforts to integrate research on plant microbiomes into teaching. She developed an undergraduate summer research program in her lab where students engaged directly in experiments to test hypotheses for how plant genotype-phenotype relationships shaped the plant microbiome. She also re-designed core undergraduate courses to engage OSU students in this work, giving them lab periods in her common garden where they formulated and tested hypotheses, and contributed to the project’s overall research goals.

Connecting real world research to learning ensures more potential future scientists have access and opportunity to pursue these interests – or even know these interests exist. Exposure to undergraduate research is proven to be a key factor in student success. In fact, in a study from the University of Puerto Rico researching Hispanic-serving institutions, students who engage in undergraduate research for just one semester increase their chances of graduation from 41% to 67%. And those who pursue undergraduate research for two or three semesters, have graduation rates over 97%.

Students Jess Arenson (left) and Forrest Walker (right) preparing leaf samples for microbial characterization using DNA metabarcoding.

Melissa Vergara is a great example of a student who is building a successful career in science thanks to early access to undergraduate research opportunities. Currently a graduate student pursuing a Ph.D. in Botany and Plant Pathology, Vergara is a member of Busby’s research lab. But when she began her undergraduate studies, she thought the only “doctors” were medical doctors.

When asked about her interest in science and how she ended up pursuing a Ph.D. having not known what it was when she started her educational journey, Vergara reflected upon her journey as a first-generation college student who started at a community college in her southern California hometown.

A chemistry professor there encouraged her to join a Bridge program that connected her with a graduate student at UC Santa Cruz who first exposed her to the idea that research was even part of the science learning experience. As part of the Bridge program, Vergara collaborated on a review paper and later when she transferred to UC Santa Cruz as a plant science major, she stayed in touch with that grad student.

“Having access to research opportunities in community college and later as a student at UC Santa Cruz, was a turning point for me,” Vergara said.  “Doing research as an undergrad cemented the concepts I was learning. I was taking a lot of classes but doing the research, doing it first-hand, spending more time with my professors, getting into scientific reading and deliberation, really reinforced those concepts that I was just brushing over in class.”

I was super fascinated by microbial ecology, so when I started thinking about the possibility of grad school, I knew I wanted to dig deeper into those issues.

Along the way, Vergara sought out more mentors and research opportunities, including a research trip to Panama where she studied fungal endophytes. It was on that trip that she was first made aware of opportunities in Busby’s lab at OSU.

“I was super fascinated by microbial ecology, so when I started thinking about the possibility of grad school, I knew I wanted to dig deeper into those issues,” Vergara added. “In Panama I worked with leaf endophytes and read about Posy’s research in this field, and this was my first direct connection to the possibility of working with her.”

Fast forward to 2023 and Vergara is now an active and important member of the team of scientists collaborating on this NSF-funded microbial research project. 

As one of the three core pillars of OSU’s land-grant mission, education is made more powerful and the learning more lasting when it is connected to emerging research like this. Further, the future of research is made better because it invites new ideas from future scientists like Vergara who may not have known this path existed. Students win. Science wins. And as a result, everyone wins.

The Future of Research

As researchers like Busby continue to build upon critical avenues of discovery and seek to create pathways for the future of science with undergraduate and graduate students, it is critical to remember that another key piece to the research puzzle is emerging technology that can speed the process of discovery.

Today, the College is spearheading a campaign to fund a new Plant Innovation Complex that will allow OSU scientists to be more competitive with the most forward-thinking research taking place in plant science around the world by investing in cutting edge tools in an intentionally transdisciplinary setting.

Despite all the progress made, scientists like Busby sometimes feel limited by the constraints of the technology available to them to take their research as far as they think it can go. For example, environmental control is a critical feature in research addressing microbiome-mediated heat and drought tolerance in plants.

Melissa Vergara, PhD candidate in the Busby lab, tending wheat plants in the greenhouse. This genetic mapping population will help Vergara determine genetic regions that influence microbiome-mediated genetic resistance.

“We can’t do some of the experiments we would like to do now because the environment is uncontrollable,” Busby added. “We have to bring plants into tiny growth chambers, studying 20 plants at a time instead of large genetic mapping populations. The cottonwood mapping population I work with, for example, includes over 1,000 genotypes, so we need large, controlled spaces to include all the members of the mapping population.”

In addition to environmental controls, any high throughput phenotyping capacity the Plant Innovation Complex might make available could be a game changer for Busby and others seeking to make connections across genotypes and phenotypes.

High throughput phenotyping (HTP) is a scientific approach and technology-driven method used in various fields, particularly in biology, agriculture, and medicine, to rapidly and systematically analyze and quantify the phenotypes of a large number of individuals or samples. This approach aims to automate and streamline the process of phenotypic data collection and analysis, making it faster and more efficient.

While technology isn’t a panacea for addressing challenges faced by scientists, it can expedite the pursuit of “what if” questions that result in high-impact discovery. Technology has always been a key player in the evolution of science. Since Galileo used a telescope in the early 1600’s to upend the belief that the sun revolves around the earth, scientists have relied upon technology developments to help expedite discovery.

In other words, if in fact research is like laundry in so far as it is never truly done – how much more efficient is our Maytag than our washboard?

Busby and her growing team of collaborators across OSU, the state and beyond make up just one example of the countless research projects taking place at any given time in the College of Agricultural Sciences. No matter what the future technical capacity allows or what the next big scientific question presents, or what new avenues of research either reveals, one thing will remain constant: research is never done.

“I always am feeling like I’m standing on the shoulder of giants,” Vergara mused when contemplating her future. “What surprises me most as I engage in this research is how quickly ideas are made. Science an evolving process. There’s so much that has already been done, and so many ideas that have come before me. I feel so grateful to be a part of the development of it and glad that I now have the knowledge and confidence to contribute to its future.”

So, while it is true that we will never have it all figured out. We will never have all the answers. And while it is equal parts humbling and meaningful to recognize that our ever-expanding universe is uncontainable. The good news is, so too is our imagination and our capacity for discovery.

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