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Small but mighty – and mighty complex

Many types of soil microbes influence crop growth, health and yields. Figuring out how to harness these tiny organisms to enhance crop production is chockfull of intriguing challenges and potential benefits, as George Lazarovits knows.

Lazarovits is research director at A&L Biologicals in London, Ont., and an adjunct faculty member in plant pathology and soil ecology at the University of Western Ontario. He and other researchers in Canada and around the world are investigating the identities of microbes that live near, on and in crop plants, determining the roles these microbes play, and exploring how to manage these microbes to benefit crops.

Microbes can help plants in significant ways. “A very large proportion of the bacteria that live in soil can actually make things that are hormonal to the plant – indoleacetic acid, gibberellins, cytokinins. These affect plant growth and development in a huge way,” Lazarovits says.

Another very valuable function is to fix nitrogen gas into a form of nitrogen that plants can use. He explains, “Bacteria are the only organisms on the planet that have a major role in nitrogen fixation. The biggest group of nitrogen-fixing bacteria is the rhizobia, the bacteria that make nodules on legume roots.”

Other important microbial activities include controlling plant pathogens, making phosphorus and other soil nutrients available to the plant, and protecting the plant against abiotic stresses like drought.

Rhizobia for non-legumes
Many crop growers are familiar with inoculants of rhizobial species (such as Rhizobium and Bradyrhizobium) for nitrogen fixation in legume crops. But scientists have also been looking into the use of rhizobia with cereals. As an example, Lazarovits highlights the work of Frank Dazzo, people from his lab at Michigan State University, and their colleagues.

Their research shows big benefits from inoculating rice crops with rhizobia. For instance, in large-scale field trials in Egypt conducted over five growing seasons, the researchers inoculated five rice varieties with seven strains of rice-adapted clover rhizobia.

These rhizobia naturally colonize rice roots in the Nile delta, where rice has been rotated with clover for centuries. In the trials, crop response to inoculation depended on the rice variety and the rhizobial strain. Inoculation significantly increased rice yields in 19 of 24 trials. Using the most effective inoculant strains, yield increases averaged 19.5 per cent, with a maximum increase of 47 per cent.

Through lab studies, the researchers determined that the rhizobia are endophytic in rice – they colonize the interior of the plant, rather than forming nodules on the roots.

Studies by Dazzo’s group and other researchers on such cereals as rice, wheat and corn show that endophytic rhizobia can provide many crop benefits. Some of the identified benefits are: higher root and shoot biomass, greater photosynthetic activity, greater water use efficiency, better nitrogen fertilizer use efficiency, greater ability to acquire various nutrients and higher crop yields.

Lazarovits sees great potential for other types of microbial inoculants, too. He and his colleagues, as well as other researchers, are working with microbes that perform specific functions in one type of plant and seeing if they can transfer the microbe, and its function, to a different type of plant. In the long run, they hope to create not only single-function inoculants, but also inoculants with groups of beneficial microbes.

He explains, “Within the next three or four years, you’re going to see a whole slew of consortia – groups of organisms with different functions that can live together happily – being put together as a family of organisms that can do all the functions the plant needs. However, one of the things researchers need to do is make sure these organisms are compatible with each other, and no one has really gone into that yet.”

In one current project, A&L Biologicals will be doing laboratory analysis for Engage Agro’s crop trials with the bacterium Gluconacetobacter diazotrophicus, or “Gd.” A British company called Azotic Technologies is developing Gd as a crop inoculant called N-Fix. Through a partnership with Azotic, Guelph-based Engage Agro is testing N-Fix’s effectiveness in several Canadian crops.

Gd is known for its nitrogen-fixing role in sugarcane. “The woman who developed sugarcane [for ethanol] as a major industry in Brazil went to farms where sugarcane had been grown for three or four centuries. She selected cultivars that performed really well in the absence of inputs like fertilizers. That allowed Brazilian sugarcane to be produced at a very low cost,” Lazarovits says.

It turns out that, in those low-input sugarcane cultivars, most of the crop’s nitrogen needs are provided by a thriving community of different microbial species living within the plant, with Gd as the most important nitrogen fixer. Studies also show that Gd has other talents like fighting sugarcane pathogens and producing hormones that promote plant growth.

Lazarovits wonders if modern breeding programs may have created crop varieties that have lost some of their ability to have beneficial microbial interactions. “In our breeding programs, we usually do the exact opposite of what was done with sugarcane in Brazil: we make it perfect for the plants we’re breeding.” However, he says some researchers are now selecting breeding lines under low-input conditions. That could lead to varieties that work especially well with beneficial microbes, and perhaps to identification of native microbial species and strains that are especially helpful.

Disease-suppressing bacteria
One of the main types of disease-suppressing microbes is a group of bacteria known as fluorescent pseudomonads – ‘fluorescent’ because they glow under ultraviolet light, and ‘pseudomonads’ because they belong to the genus Pseudomonas. James Cook and his students at Washington State University carried out four decades of studies related to these bacteria. This research sprang from the surprising observation that take-all, a serious fungal disease of wheat, could be eliminated from a field by growing continuous wheat.

“The researchers found that after six or seven consecutive wheat crops, take-all disappears,” says Lazarovits, who was one of Cook’s students. “Not only that, if you take some of the soil from the field where the disease has disappeared and mix it at a ratio of 1 to 99 with a soil that has the disease, then the disease disappears from that soil.”

Cook’s group eventually figured out that fluorescent pseudomonads were causing the take-all suppression. “And the most important Pseudomonas species were the ones that were making a very large number of antibiotics. These antibiotics, which are on the wheat plant’s roots, prevent the take-all fungus from affecting the plant,” Lazarovits explains.

“Repeated cultivation of wheat allows the Pseudomonas bacteria to reach a critical mass in the soils, and this critical mass then becomes self-sustaining.”

Studies by other researchers have identified various fluorescent pseudomonad species that are effective in controlling other diseases in other crops. In fact, Lazarovits notes that DNA testing for Pseudomonas populations can be useful for diagnosing and tracking soil health. “You can now test soil samples to see if they have sufficient amounts of this antibiotic production capacity to be disease-suppressive.

So crop growers who have built up an ecosystem with a disease-suppressive soil are now diagnosing their soil to have this health condition, and they are checking to be sure that crops they add to their rotation don’t destroy those organisms.”

Rotation explorations
The fact that wheat monocropping controls take-all goes against the common recommendation that diverse rotations are better for reducing disease – and yet certain pathogens do tend to build-up in monocropping systems.

“As far as I’m concerned, we still don’t really understand what we’re doing in the ecosystem in agriculture. We make assumptions, and a lot of times our assumptions are wrong,” Lazarovits says. Soil microbial communities are often very complex, with huge numbers of microorganisms and a wide diversity of species. And the communities are dynamic, changing as field-scale factors like agronomic practices and weather patterns change.

So, what should crop growers do if they want to try to develop a more beneficial agro-microbial ecosystem in their own fields? Lazarovits suggests adding green manures to their rotations. “We have seen that adding green manures to the soil has a huge beneficial effect. It is a way of feeding the soil and keeping the microbial population levels up high.”

A&L Biologicals is working on green manure trials with Dean Glenney, a Dunnville-area farmer with an innovative, high-yielding cropping system. Using no-till, controlled traffic practices, Glenney grows a corn-soybean rotation, with the two crops grown in alternating strips. Over the years, his production system has gradually built up beneficial soil microbial populations. However, certain pathogenic microbes have also built up, which may be preventing Glenney’s crops from reaching their maximum yield potential. So Glenney and Lazarovits want to see if green manuring would suppress those pathogens – and enable Glenney’s 300 bushel corn yields to get even higher.

Economics can be a concern with green manures because there is no harvested crop. According to Lazarovits, Glenney has built planting equipment for underseeding a green manure crop once the corn crop has reached the right stage. That way, Glenney could earn money from the corn crop while also having a green manure.

Lazarovits hopes the green manure trials with Glenney will also shed light on what other growers could do to increase their crop yields through boosting beneficial microbes. In the future, he sees exciting potential with intercropping.

“Although the biological mechanisms are not well understood, many farmers are looking into green manures and especially intercropping where, for instance, they plant potatoes and also plant three or four other crops in between the potato rows. People used to think an intercrop is a crop competitor, but they are finding that intercropping with different types of crops actually reduces pathogens and enhances the potato yields.”

He adds, “Farmers do more experimentation than scientists can even imagine.”

October 9, 2015
By Carolyn King


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