Microbiology on the Farm: Protecting Crops, Livestock and Fish from Diseases

Dec. 15, 2021

Image of the Fall 2021 issue of Microcosm magazine.

From the Winter 2021 issue of "Microcosm."

Infectious disease outbreaks are always a major health concern. Pathogens that affect humans naturally get most of the headlines, but perhaps as important are the ones that affect and threaten the global food supply. Diseases that impact plant crops are estimated to cost $220 billion annually worldwide, while the U.S. Department of Agriculture estimates that livestock-targeting pathogens result in approximately $17.6 billion annually in losses. Beyond the financial cost, these diseases also result in less food being available, a gravely serious issue when more than 800 million people worldwide already face food insecurity.

Given the high potential for devastating economic, ecological and epidemiological outcomes, farmers, policymakers, public health officials and researchers have collaborated for years on approaches to control the spread of agricultural infectious diseases. However, as pathogenic microbes continue to proliferate and cause damage, there is a pressing need to reexamine existing methods. Are these approaches effective? Are farmers best equipped to handle the current and future challenges facing the agricultural industry? If not, what else can be done?

Cull 'em All

In 2015, an outbreak of measles at Disneyland led to more than 125 confirmed individual cases. While the situation resulted in several immediate responses from policymakers and public health authorities, at no point was there a suggestion to euthanize the approximately 2 million people who visited the Southern California amusement park during that 2-month period. Yet that is exactly the kind of blunt approach often taken when it comes to halting (or slowing) the spread of infectious disease in plants and animals. From boars in Germany to badgers in the United Kingdom to minks in Denmark, governments have forced farmers and producers to carry out broad culls of entire populations that have potentially been exposed during an outbreak, eliminating hosts (and hopefully pathogens) in the name of public health.

Image of a head of cattle roaming a grazing range.
Diseases that impact livestock are estimated to cause more than $17 billion in losses annually.

Unfortunately, studies of animal-culling practices have found that such strategies, while crudely effective from a cost-benefit perspective, are not economically sustainable. Besides the financial factors, there are also social and personal considerations to take into account. "It's a hard decision to have to make to euthanize an animal," says Jackie Boerman, Ph.D., assistant professor of Animal Sciences at Purdue University. "I don't know very many farmers that get into animal agriculture not really liking animals." Farmers aren't the only ones with conflicted feelings. The recent badger-culling program in the U.K., aimed at eliminating the spread of bovine tuberculosis, generated massive public outcry (drawing in luminaries including Sir David Attenborough and Queen guitarist Brian May) that has forced the government to backtrack on its plan.

Similar challenges arise when it comes to culling (or "roguing") plant crops. According to Robin Choudhury, Ph.D., an assistant professor in the School of Earth, Environmental, and Marine Sciences at the University of Texas Rio Grande Valley, "Remov[ing] diseased plants from individual farms or plots ... has been shown to be really effective when done in a timely manner." However, at larger scales, the efficiency of roguing drops, because, as Dr. Choudhury notes, "by the time that you notice a new pathogen in a region, it is too late to get rid of it completely from a new region." The decision about whether to rogue also forces farmers into daunting financial decisions. There is an "economic threshold for deciding when to cull" an infected population, states Justin Knopf, a fifth-generation grain farmer from Salinas, Kan. "A lot goes into the decision," he points out. "Is the disease hitting ahead of harvesting season? What is the yield potential of the crop? What is the weather outlook?"

New Treatment Options

Faced with the looming prospect of increased disease prevalence, researchers, farmers and regulators alike are being forced to adopt a new mindset. Instead of always defaulting to culling as a solution, Dr. Choudhury advises that a better strategy is to focus on mitigation and management practices, which generally mean antibiotics, plant pesticides and (in animals) vaccines. Unfortunately, "there's nothing profitable about mitigation strategies," according to Jeff Baker, a dairy farmer from Friendship, N.Y., "because you've already lost money." Beyond the cost of the drug treatments, Baker points out that animals who have received treatment typically have reduced production capabilities, resulting in lower yields and, ultimately, profits.

Instead, there is a growing preference for what Knopf refers to as "beneficial biology" — preventive behavioral strategies to combat disease, instead of continuing to rely so heavily on the use of drugs (whether synthetic or natural). As he explains, "The most significant measure to prevent disease is a holistic approach to [a] crop system" that relies on diverse crops, crop rotation and specialized cover crops.

Behavioral interventions are similarly effective in aquaculture. As Ted Meyers, Ph.D., state fish pathologist for the Alaska Department of Fish and Game, explains, fish-hatchery operators in Alaska "are cognizant of good fish culture." What that means in practice, according to Dr. Meyers, is that these operators "provide adequate space to rear fish so there's less density, less crowding. They examine their fish on a regular basis, watching very carefully when these fish are rearing, adding a water supply that is free of [pathogens]." At the same time, adds Dr. Meyers's colleague Jayde Ferguson, Ph.D., there is "very, very little antibiotic treatment." The result, says Dr. Meyers, is that "we don't see as many [disease] cases perhaps as some of the pathologists do in the lower 48 [states], because our hatcheries are performing better."

Another helpful adaptation is to use drug treatments more clinically. "On those animal ranches ... we're creating these antibiotic-resistant pathogens by overuse of antibiotics as prophylactics," states Mo Kaze, Ph.D., a fellow at the Department of Energy's Joint Genome Institute. "I've seen this in action, where the vet just goes through and hits every single animal with antibiotics, regardless of whether or not they have an infection." Dr. Boerman echoes the call for restraint. "We want to try to do our best to use antibiotics when they're going to be effective, and not use antibiotics when they're not needed," she says.

A major issue complicating these decisions is that of climate change. "Climate change is definitely going to be a factor for disease," states Dr. Choudhury. "When we have that kind of increased variability," he adds, "that means that we have to prepare our crops differently." As temperatures and humidity levels increase, Dr. Kaze points out that "we're creating these environments unintentionally that ... the microbes that are not beneficial to us are just going to love." "Parasites," she adds, "are going to be thrilled." Even geographic isolation won't be enough to stave off the impacts of climate change. "We'll be getting fish species that we don't see (in Alaska) ... extending their ranges," predicts Meyers. "They're going to bring with them, I'm sure, certain things we've never seen before as far as pathogens go."

What Can Microbiologists Do?

When asked how scientists could be of help to him, Baker points to tracking and detection of pathogens and disease on his farm. Respiratory diseases have been the main source of outbreaks among his cattle; unfortunately, the only way to properly identify (and treat) this kind of disease is, as Baker explains, "to euthanize [cows] and send samples to the lab." Rather than continuing to rely on this slow, costly process, he wonders whether it is possible "to develop a test that could just take blood samples from a live animal to identify and specify which disease is being dealt with."

Knopf echoes the call for better real-world applications of microbiology on his grain farm. "What would be helpful to me," he says, "is having more information and a better understanding of what … the beneficial microorganisms [are] that can help plants be healthier (naturally) so that they can overcome disease without the use of outside synthetic inputs."

Dr. Choudhury supports this natural approach. "I think we're heading into the region of actually being able to do proper biological control," he claims. Dr. Kaze agrees. "In many ways, it replaces those traditionally chemically synthesized pesticides," she says. "It's cheap, it's effective, it's used all over the world [and] it's safe for consumption."

But perhaps the most helpful advancement would be less about hardcore science and more about building better relationships between the different stakeholders. As Dr. Ferguson states, "microbiologists need to know about the culture. They need to know about the industry and how things are done so they can apply their microbiology knowledge in context with what's being produced, how it's being produced [and] what are real risks and real threats."

As with so many issues, the first step toward better disease-management may be as simple as having a conversation.

Author: Geoff Hunt, Ph.D.

Geoff Hunt, Ph.D.
Geoff Hunt earned his Ph.D. in molecular biology from Princeton University.