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Microbial management

Way Back Wednesday – Farming Smarter Magazine Spring 2016

A new tool in crop input efficiency

by Lee Hart

While earth worms are important indicators of soil health, it is understanding and using the millions and millions of microscopic bugs in the soil that will take western Canadian farmers to the next level of crop production efficiency, says an Agriculture Canada researcher.

Microbe slide
Nature Reviews Microbiology 9,628 Sept. 2011 Credit: Dr. Lori Phillips

The bug reference is an over simplification of the complex biological communities that live in the soil, but understanding and making better use of the invaluable role of soil microbes will help farmers fine tune management over the coming years, says Dr. Lori Phillips, a soil microbiology researcher at the Harrow Research and Develop Centre in western Ontario.

“It is just in the last few years that we have had the affordable tools to begin to indentify and better understand the role of soil microbes — bacteria and fungi,” says Phillips, who just returned to Canada after working for five years on similar research in Australia.

“Up to 50 per cent of applied fertilizer nitrogen, for example, may be unavailable for crop uptake,” says Phillips. “Some nitrogen is lost from the soil by leaching and gassing off, while some is locked up in the soil in forms unavailable for plant use. Both processes are driven by soil biological communities. Our research looks at how these communities regulate nitrogen cycling in the cropping system.”

The whole concept of managing microbes in the soil is under study, not only by a network of researchers in Canada, but around the world, says Phillips. The objective is to eventually develop on-farm management prescriptions that not only enhance populations of beneficial microbes, but also learn to how to make the best use of these microbes.

“Hopefully we can develop prescriptions for such things as the timing and placement of fertilizer and even the use of different cropping rotations that will help farmers realize greater efficiency from these inputs,” says Phillips. “In Australia, there are some extreme examples where nitrogen use efficiency is extremely low ranging from 50 to 90 per cent. In Canada it may be more like 50 per cent. If we can better manage the timing and placement of that fertilizer so soil microbes can convert it to plant available nutrients, it can represent a huge benefit to producers.”

Although millions-strong in number, soil microbes are an unseen force performing several different functions in the soil — most are critical to the biological process of producing crops. These functions include: cycling carbon by photosynthesis and decomposition; regulating plant nutrient supply and loss (e.g. N, P, K, Fe); capture and release of greenhouse gases such as carbon dioxide, methane and nitrous oxide; improvement of soil structure (aggregate stability); degrading pesticides; helping to regulate water quality (e.g. filters nutrients); and suppressing soil borne diseases. So understanding which microbes do what and how they do it is important knowledge.

So looking at those that specifically process nutrients, for example, it is important to know how they work. By first identifying what these microbes are — giving them names as Phillips says, then understanding what they do in the soil, researchers can help direct farm management practices that make greater use of the beneficial microbes and either avoid or, at least, not encourage the non-beneficial microbes that actually contribute to fertilizer losses. .

“Particularly when we talk about fertilizer placement we can influence microbial populations,” she says. “With the proper placement we can enhance the populations we do want and not feed those we don’t want. One analogy is rather than throwing out hay that can be eaten by deer, we can place it so it is only available to cattle, where we want it.”

Microbe management is a new level of fine-tuning crop production management, says Phillips. It won’t likely lead to doubling crop yield, “but even if it leads to a five or 10 per cent increase in nitrogen use efficiency, that is significant benefit to farmers,” says Phillips.

 Studying soil microbes is an exacting process. Phillips uses molecular tools in the complex task of identifying and “naming” the thousands of microbial communities found in just a tablespoon of soil. Advancements in technology have made the process of DNA sequencing an affordable tool in identifying these microbial communities, says Phillips.  

Using those tools she, and other researchers are able to identify the different microbial communities and ultimately their role in processing nutrients in the soil.

“Various microbial communities are stratified in the soil,” says Phillips. “Different communities live at different levels in the soil. So by knowing who they are, what they do, and where they are, we can advise farmers about how to make the best use of their ability to process nutrients.”

Phillips says making more effective use of soil microbes won’t involve dramatic changes in farming practices, but is more about tweaking processes that are used today.

“It involves changing management practices slightly,” she says. “It may involve depth of fertilizer placement, the strategic use of urease inhibitors or the timing of fertilizer…if we tweak them slightly we can gain N-use efficiency.”

Again referring to the Australia experience, Philip says some of the most innovative farmers were already conducting test strips on their fields to evaluate the effect of management changes.

“They can use conventional seeding equipment and perhaps just make changes in fertilizer placement to observe changes,” says Phillips. “By knowing what works or doesn’t work, it can give them confidence to try different treatments.

“With timing, for example, we saw with canola, that a split application of fertilizer might be more effective in increasing fertilizer efficiency because microbes are at one location at the time of seeding, but a different location later in the season.”

Phillips says the prescription phase of this research is still some years away. “It has only been in the past five to 10 years that we have had access to affordable research technology,” says Phillips. “So really we are just in the early stages of identifying these microbial communities and understanding their specific roles in processing nutrients.

“But, the prescriptions will come in the not too distant future that will help farmers target crop production management to get optimum performance out of soil microbes and increase efficiency of their crop inputs.”