Blowin’ in the wind
Many crop growers know about the use of unmanned aerial vehicles (UAVs), or drones, for activities like crop scouting. But UAVs are also a great tool for detecting and tracking airborne spores, bacteria and other microorganisms that cause crop disease.
The resulting information can have such practical applications as helping in on-farm disease management decisions, contributing to early warning systems for major diseases, evaluating the effectiveness of disease eradication efforts, and tracking down the sources of disease outbreaks.
“The field of aerobiology, which is the study of the flow of life in the atmosphere, has lacked appropriate tools to get after organisms that are flying high in the sky. UAVs have really become an important tool in that arena,” David Schmale, an associate professor at Virginia Tech, says.
According to Schmale, the use of UAVs in aerobiology got off the ground through the work of United States Department of Agriculture (USDA) plant pathologist Tim Gottwald back in the 1980s. Schmale notes, “Tim Gottwald stuck a little rotating spore trap underneath the wings of a biplane, along with some little insect nets that he could remotely swing open, and he started buzzing peach and pecan orchards. His work was the pioneering work to get unmanned systems to track the movement of plant pathogens and also insects in the atmosphere. So he is the godfather and the real motivation behind all that we do.”
The Schmale Laboratory has been working on the use of UAVs in aerobiology for over a decade, making important strides forward in both the technical aspects of how to conduct this type of research and in discoveries about plant pathogens and their transport tens to hundreds of metres above farm fields, across thousands of kilometres. Depending on their study objectives, they can sample the entire microbial community along the UAV’s sampling path or they can tailor the sampler to selectively collect certain species. They can sample at a single altitude or multiple altitudes to find out where and how the microbes are moving. And they can sample at different times of the day and the year to learn about the timing of pathogen transport and deposition.
A key early advance at the lab was their development of a fixed-wing UAV (a UAV that looks like a little airplane) with its own onboard computer system. “Although technologies like autonomous systems are readily available today on most unmanned systems platforms, they were in their infancy about 10 years ago,” Schmale says.
“In this case, we had a small autopilot computer about the size of a cell phone that had been integrated into a UAV and allowed the UAV to follow prescribed paths through the atmosphere at really tight altitudes. That was really an important milestone for us in terms of engineering.”
And this engineering advance enabled important discoveries about pathogen movement.
Some of those discoveries involve Fusarium pathogens. “The genus Fusarium contains some very nasty plant and animal pathogens, and many of them produce mycotoxins. We have a really good selective medium for Fusarium that we can take for a ride on one of our aircraft, and we’ve collected all sorts of different Fusarium species,” Schmale explains.
“The first discovery was about a very important plant pathogen of wheat, barley and corn, Fusarium graminearum. We were able to show that isolates we had collected upwards of 40 to 300-odd metres above the surface of the earth were able to cause disease and produce mycotoxins.
“And one of the isolates produced a really unique toxin that we hadn’t discovered in any of our ground-based populations in Virginia. So this unique isolate was buzzing through the atmosphere over Virginia, perhaps from somewhere pretty far away, which was really exciting and had important implications for biosecurity efforts.”
These findings confirmed the long-distance spread of Fusarium graminearum spores and the potential for this type of transport to contribute to increased disease risk and to changes in Fusarium populations that could affect human health.
Surprisingly, the UAV samples from this research include many previously unknown Fusarium species. Schmale says, “One of the more striking aspects of that work is that about half of any given population that we’ve collected appears to represent new or understudied species. So, at least in terms of Fusarium, quite a bit remains to be discovered in the air. Many of these potentially new species could also be important pathogens that just haven’t yet been studied or uncovered in some agricultural system.”
A big part of the lab’s current work relates to the use of UAV sampling data to understand atmospheric dynamics and to help predict the regional-scale movement of airborne crop pathogens. One of Schmale’s engineering colleagues at Virginia Tech, Shane Ross, is modelling atmospheric features called Lagrangian coherent structures, or LCSs, which are like waves in the atmosphere. Schmale and Ross came up with the idea of using Fusarium sampling to track what the LCSs are doing as a way to confirm the modelling work. He notes, “We were the first to show that LCSs shuffle along Fusarium populations and modulate their movement over long distances in the atmosphere.”
The Schmale Lab is also studying the trajectories of airborne pathogens, seeking to identify their sources and destinations. As part of this, the researchers are doing release-recapture experiments, where they release identifiable spores in a field and find out where those spores land to determine pathogen movement patterns.
Monitoring fungicide resistance in Quebec
A new Canadian project will soon be using UAV sampling to monitor for fungicide resistance in Botrytis, an onion pathogen, in southern Quebec.
“We want to monitor if resistance is building up in the pathogen’s population in the region. We’ll use this information to provide the growers with information about which types of fungicide are no longer efficacious,” Bernard Panneton, who is leading the project, says. He is a research scientist at Agriculture and Agri-Food Canada’s Saint-Jean-sur-Richelieu Research and Development Centre, a horticultural research facility that specializes in field vegetable crops.
“In our research centre, there is a huge expertise in using ground-based samplers to monitor diseases in horticultural fields. During the last three years we had a project using ground samplers, placed about one metre above the ground and on towers up to 10 metres high, to monitor how spores from fungal diseases are emitted from a field and dispersed over the area and eventually go higher in the air and move away. We found that even at 10 metres above the ground, we can collect quite large samples if you do the sampling at the right time and in the right way,” he says.
To monitor for fungicide resistance, the researchers need information on what is happening at a regional level, so they want samples from higher than 10 metres. “With spore sampling, the higher up you are, the further back you see – the spores come from a longer distance,” Panneton notes. Plus they will need to sample large volumes of air. “When you are at some distance above the ground, above 40 or 50 metres, the density of spores is pretty low. So you have to sample for a long time with an efficient sampler to collect some spores on your sampler.”
UAV sampling can meet these needs – a UAV sampler can sample a much larger volume of air than a ground-based sampler, and it can sample the air at specific altitudes high above the ground.
Panneton’s research team will be using an octocopter, a little helicopter-like UAV with eight rotors. It has a small onboard computer with GPS, so the researchers can upload its flight path. “This technology is getting fairly cheap, and it is a bit easier to use than a fixed-wing UAV. With the fixed-wing type, you need a place to take off and land. With the octocopter, you don’t need a landing strip. And the electric motors are fairly easy to service.”
The project’s first step will be to develop the necessary technologies to conduct the Botrytis sampling. For example, the little octocopter is limited in terms of how much weight it can carry, so the researchers will have to develop a lightweight sensor.
They’ll also need to develop a way to plan the UAV’s flight paths to collect samples that will be representative of the region. Panneton says, “We will use a map showing where the onion fields are in the region plus forecasts of meteorological conditions to see where the wind is coming from. From this information, we will have to find a way to design a proper flight path so we increase the probability of collecting spores. We are hoping to detect fungicide resistance when the resistant proportion of the population is fairly low, about 10 per cent of the population. So we will need a fair amount of the spores to do that.”
Panneton plans to conduct the sampling in August when spore emission from the onion fields is at a maximum. “We think we can achieve a good sampling program with perhaps two flights at two different dates.”
The sky’s the limit
Looking ahead, Schmale and Panneton see intriguing possibilities for UAV sampling.
Panneton is excited by the ability of UAVs to work at different altitudes and scales. “I think there is a future for a multi-scale approach where first you look at a larger region to get an understanding of the overall pathogen situation. If you see that something is happening and it seems to be coming from a particular area, then you can fly right there and take a point sample to confirm your hypothesis. And this approach can also work for weed [pollen], insect pests and other things we can find in the air.”
On-the-go pathogen reporting is another potentially important possibility. The Schmale Laboratory has been experimenting with a portable biosensor to do this. “We were interested in being able to collect and analyze a sample in the atmosphere while the drone was flying and to communicate that analysis down to a ground control station, which is essentially a computer on the ground that is talking with the aircraft while it’s flying,” Schmale notes.
Unfortunately, the sensor they’re using costs about $30,000 so it’s not a practical option for most agricultural uses at present. “However, those sensor technologies will continue to decrease in size and hopefully cost,” he says. “For the future, it opens up many exciting applications like being able to do source tracking while you’re in the air, so essentially sniffing out the plume of an agent, and continuing to follow the concentration gradient until you find the source of that agent.”
Another potential application of UAV sampling is for on-farm disease monitoring. Schmale says, “Imagine you’re a potato grower with thousands of acres of potatoes and you are really worried about a particular pathogen that might be blowing into your potato fields from somewhere else. UAV sampling can do something that a ground sampler can’t do – it can sample a very, very large volume of air. So you can essentially sniff over your entire farm, collect a very large volume of air and determine whether or not a disease agent is there.”
At the Schmale Laboratory, the latest UAV research ventures are heading in a new direction: bioprecipitation. “Some of our recently funded work is focused on a rather narrow group of microorganisms [called microbial ice nucleators]. Some of these microbes reside in clouds, while others live on leaf surfaces and in the soil and become airborne. They express interesting proteins that allow water to freeze at higher temperatures and have been associated with global precipitation events,” Schmale explains.
“The idea that a microorganism can be determining whether or not it is going to rain, hail or snow is pretty exciting.” His research on these microbes could eventually lead to improved precipitation predictions, and perhaps even contribute to approaches to weather modification. For instance, some researchers are proposing the idea of planting crops that are hosts to these microbes as a way to increase precipitation in arid areas. “Potentially we could do things on our land surface to change the weather, which is an interesting concept and likely to be very important in the coming decades.”
April 7, 2016 By Carolyn King