AgronomyNext-Generation Sequencing

Next-Generation Sequencing

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[deck]A powerful scientific technique for studying soil bacteria could help combat common scab in potatoes.[/deck]

Soil is sometimes referred to as the last frontier because so little is known about the microscopic life that teems within it. What we do know is that a small handful of dirt typically contains thousands of tiny microorganisms, many of them still unidentified by science. Because the crops we grow and food we eat depend so heavily on the health of the soil, scientists around the world are working hard to unlock the mysteries of the tiny life forms that inhabit it.

One of these soil scientists is noted potato researcher Claudia Goyer, a molecular biologist at Agriculture and Agri-Food Canada’s Potato Research Centre in Fredericton, N.B. She and her team at the Potato Research Centre plan to initiate research next year into analysis of microbial communities using a technique known as next-generation sequencing. Their work will focus specifically on environments conducive to common scab in potatoes, a disease caused by filamentous bacteria that results in brownish lesions on tubers. Although the lesions are not dangerous and usually don’t affect yields, they do make potatoes less aesthetically pleasing to consumers and therefore, unsellable.

“Consumers are not interested in buying unattractive potatoes,” says Goyer. “In the industry, potatoes cannot be sold if they’re covered in more than five per cent lesions. It’s a big loss for growers, and there’s still no means to control common scab.”
“In agriculture, we don’t understand why certain fields are diseased when others are not,” says Goyer. “There are certain microbial communities that seem to be important when it comes to disease and disease suppression. What we’d like to do is to better understand what are the factors — the biological aspects i.e the microbial communities — in the field that promote or are conducive to disease in potatoes.”Using the next-generation sequencing technique, Goyer plans to compare microbial communities from 20 fields — 10 where common scab is present and another 10 where it isn’t — to determine which species of microorganisms are present in each field. Once the makeup of each microbial community has been determined, the researchers will then test to see how each field responds to different management practices such as crop rotation, as well as compost and manure applications. It is their hope that they will learn how to manipulate those communities to create not only healthier soil, but also suppressive soil that can actually counteract disease.

The project, which is now under review, should begin sometime in 2014.

Next-Generation Sequencing Explained

What exactly is next-generation sequencing? Goyer offers this primer on this powerful technique that promises to revolutionize the way soil is studied.

When scientists first began studying bacterial organisms at the beginning of the 20th century, bacteria were grown on solid mediums on plates. Because of the limitations of this method, only a small fraction of the bacteria could be cultivated for analysis, says Goyer, which meant entire microbial communities were left unstudied.

Later, scientists began sequencing genetic material to identify bacteria at the species level, but the process was painstakingly slow and extremely expensive. For example, decoding the first human genome, or complete set of genetic material, cost millions of dollars and took 10 years to sequence, says Goyer.

Today, using next-generation sequencing, scientists can find anywhere between 5,000 and 10,000 different species of bacteria in one gram of soil. In just one reaction, they can, in fact, find entire bacterial communities, a process that costs a mere $100, says Goyer.

“Next-generation sequencing is a tool that is opening a lot of new doors in terms of research because scientists get a much more precise estimation of what communities exist in the soil,” she adds. “And next-generation sequencing isn’t just for soil. It’s opening doors in the world of medicine, as well.”

The science behind next-generation sequencing is complex, but basically it involves gathering and referencing genetic sequences with sequences from scientific databases. Some of these sequences may be related, but many are not. The amount of information retrieved in one sweep can be daunting, so to organize it, scientists use something called bioinformatics, an interdisciplinary approach for storing, retrieving, organizing and analyzing biological data.

To get a visual, try to imagine a box full of puzzle pieces. Even though many of the pieces are from different puzzles, their pictures are similar, which can make it extremely difficult to piece them together. Bioinformatics acts as a reference tool for putting the puzzle together. It groups sequences that are known or are similar, and sets the others aside.

Even if the researchers are unable to identify taxonomically specific bacterial species, the technique allows them to see which ones are present in healthy soils. The bacteria can then be followed closely from field to field and changes in communities measured to see how they are affected by different management techniques.

The common scab pathogen is called Streptomyces scabies, a filamentous bacteria which causes brownish lesions on potatoes.

A Game Changer for Agriculture

According to Goyer, this research could be a game changer for the agricultural industry. “My guess is that if you get a healthy field you should also get a better yield,” she says. “You’re at least reducing the number of potatoes that are not sellable because of common scab.”

Glen Shaw, executive director of the Soil Conservation Council of Canada, agrees. “It’s very valuable information on determining how soil health can be improved,” he says. “There are millions of soil microorganisms. Understanding which are the beneficial ones and which are the ones that impact crop yield in a positive way or a negative way is extremely important.”

Shaw says there’s great value in crop rotation, and while he understands that crop rotation breaks disease cycles and leads to increased organic matter and therefore, increased yields, he doesn’t fully understand why.

“Increasing a rotation from two or three years to a longer rotation of four to five years [has] been shown to increase yields and reduce fertilizer needs, but I don’t think we understand exactly what’s happening,” he says.

There are millions of soil microorganisms. Understanding which are the beneficial ones and which are the ones that impact crop yield in a positive way or a negative way is extremely important.

– Glen Shaw

“One of the challenges is how you measure soil health. In the past, measuring soil organic matter was one factor that was used. There hasn’t been as much research on the microorganisms and their populations, but that kind of work is increasing,” Shaw continues. “It’s extremely important research to understanding the long-term sustainability of soils in Canada.”

Matt Hemphill, executive director at Potatoes New Brunswick, believes Goyer’s research could conceivably enable farmers to tackle problems long before they manifest in the potato field. “The micro level obviously tells us stuff that we might not necessarily see with the naked eye for two to three years down the road,” he says.

And the days of broadcasting pesticides, insecticides and fertilizers, says Hemphill, are coming to an end. “We’re looking to do more precision agriculture, which obviously has less of an impact on the environment, has a smaller carbon footprint and ultimately boosts yields and profits for growers,” he explains. “We’re looking to do variable rates, meaning parts of the field may not require as much nitrogen as others, as an example.”

“It’s obvious that soil is our No. 1 resource when it comes to planting potatoes and other rotation crops,” Hemphill continues. “Without soil health and without the science behind the future of soil health and precision agriculture, then we have no future. What Goyer is doing is very important to the future of farming here in New Brunswick.”

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