The work, published in the March 15 issue of Nature, raises the possibility of probiotic, microbe treatments for plants to increase their efficient use of phosphate. The form of phosphate plants can use is in danger of reaching its peak – when supply fails to keep up with demand – in just 30 years, potentially decreasing the rate of crop yield as the world population continues to climb and global warming stresses crop yields, which could have damaging effects on the global food supply.
“We show precisely how a key ‘switch protein’, PHR1, controls the response to low levels of phosphate, a big stress for the plant, and also controls the plant immune system,” said Jeff Dangl, John N. Couch Distinguished Professor and Howard Hughes Medical Institute Investigator. “When the plant is stressed for this important nutrient, it turns down its immune system so it can focus on harvesting phosphate from the soil. Essentially, the plant sets its priorities on the cellular level.”
Dangl, who worked with lead authors, postdoctoral researchers Gabriel Castrillo and Paulo José Pereira Lima Teixeira, graduate student Sur Herrera Paredes and research analyst Theresa F. Law, found evidence that soil bacteria can make use of this tradeoff between nutrient-seeking and immune defense, potentially to help establish symbiotic relationships with plants. Bacteria seem to enhance this phosphate stress response, in part simply by competing for phosphate but also by actively ‘telling’ the plant to turn on its phosphate stress response.
In recent plant biology studies, there have been hints of a relationship between plant phosphate levels and immune system activity – a relationship that some microbes can manipulate. In the new study, Dangl and colleagues delved more deeply into this relationship, using mutant versions of Arabidopsis thaliana, a weed that has long been the standard “lab rat” of plant biology research.
In one experiment, Dangl’s team found that Arabidopsis plants with mutant versions of the PHR1 gene not only had impaired phosphate stress responses, but also developed different communities of microbes in and around their roots when grown in a local native North Carolina soil. This was the case even in an environment of plentiful phosphate – where phosphate competition wouldn’t have been a factor – hinting that something else was happening in the plants to trigger the growth of different microbial communities. The researchers found similar results studying PHL1, a protein closely related to PHR1 with similar but weaker functions.
In another experiment, in lab-dish conditions, the researchers colonized roots of sterile-grown normal Arabidopsis plants with a set of 35 bacterial species isolated from roots of plants grown previously in the same native soil. In these re-colonized plants, the phosphate stress response increased when exposed to a low-phosphate condition.
Investigating further, the team showed that PHR1 – and probably to a lesser extent PHL1 – not only activates the phosphate stress response but also triggers a pattern of gene expression that reduces immune activity, and thus makes it easier for resident microbes to survive.
The findings suggest that soil-dwelling microbes have figured out how to get along with their plant hosts, at least in part by activating PHR1/PHL1 to suppress immune responses to them. Dangl’s team also thinks these microbes may even be necessary for plants to respond normally to low-phosphate conditions. It could be possible, then, to harness this relationship – via probiotic or related crop treatments – to enable plants to make do with less phosphate.
“Phosphate is a limited resource and we don’t use it very efficiently,” said Dangl, who is also an adjunct professor of microbiology and immunology at the UNC School of Medicine. “As part of fertilizer, phosphate runs off into waterways where it can adversely affect river and marine ecosystems. It would be better if we could use phosphate in a way that’s more efficient.”
This funding will allow the company to introduce to the market laser-induced breakdown spectroscopy (LIBS), a technology that allows for faster and more accurate data at lower cost. The goal is to provide producers with the exact amount of fertilizer needed and thereby avoid the overuse of chemicals.
The technology was developed by Logiag in 2015, in collaboration with the National Research Council of Canada (NRC) and the support of its Industrial Research Assistance Program. This investment from the AgriInnovation program, a $698-million initiative under the policy framework, will help Logiag create 45 jobs over five years.
Researchers at the University of Guelph are looking at the connection between soil biodiversity and soil health using new research, along with data collected from a long-term cover crop trial dating back to 2008.
“We are looking specifically at soil health,” explains research lead Kari Dunfield, an associate professor at the University of Guelph and a Canada research chair in environmental microbiology of agro-ecosystems.
Attention to soil health has increased in recent years as producers look for ways to decrease inputs and increase quality and yields.
We’re talking about soil health a lot in agriculture, and farmers often ask me ‘Is my soil healthy?’ ‘What can I do to keep my soil healthy?’ ” Dunfield says. “However, it’s hard to measure that so what we need to do is measure indicators. If there’s less erosion or more fertility, can we say that’s a healthy soil?”
And, while the researchers know soil microbes are important, they don’t know if greater soil diversity is actually healthier.
“Healthy soil does better under certain conditions like drought and disease pressures, but the science linking soil health to soil microbes is not there,” Dunfield says. “We don’t know if a more diverse soil is a healthier soil.”
So, the researchers are looking at that in conjunction with research Laura van Eerd, an associate professor at the University of Guelph who specializes in nitrogen fertility and cover crops, is doing in Ridgetown involving the impact cover crops have on soil health.
“In Ontario, we are not entirely clear what cover crops are actually doing for the system,” Dunfield says. “They might help with erosion but we don’t see a huge spike in microorganisms. We’re adding on to Laura’s research and looking at the bacterial and fungal community of those systems.”
Funded by the Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA), the project began in 2015 and involves planting rotation vegetable crops at Ridgetown during the growing season. “The cash crop this year is tomatoes,” Dunfield says. “At the end of the year, we’ll put in five cover crops.”
Then, five or six times throughout the year, the researchers take soil from the system and graduate student John Drummelsmith extracts the DNA to look at the soil bacterial and fungal communities and quantify them. This data, Dunfield says, will tell them if fungal and bacterial communities are going up or down depending on the cover crop.
“Some people suggest in healthy bacterial-fungal ratios, fungi should be higher,” she says. “We’re going to look at that using DNA, next generation sequencing. This tells us what bacteria and fungi are there.”
Or, in other words, what the diversity of the system is. Because of van Eerd’s project, Dunfield and Drummelsmith have yield and soil measurements as well, so they will be able to see if the communities are shifting and if there is indeed a link to the soil.
“So we can say yes, more soil diversity is related to cropping systems that produce higher yields,” Dunfield says.
Dunfield and her team began sampling in October 2015. This year, they took samples in May, June and August and plan to take a couple more this fall. Early findings show there is indeed some difference in microbial communities under different cover crops.
“We saw an increase in bacterial population with the radish and rye combination cover crop,” Dunfield says. She adds that a couple – oat cover crop and radish and rye cover crop – increased fungal populations. “That’s compared to a no cover crop situation.”
She points out the cash crop had already been harvested for the October 2015 sampling event. More recent sampling should answer the question, “Do we see the same changes when the cash crop is there or is it transient with crop gone?”
More research to come
The researchers recently received additional funding from the Grain Farmers of Ontario to expand the project to more than one site.
“We started in one soil system and this will allow us to expand into other systems to see if we find the same results,” Dunfield says. “We are planning, in next field season, to expand to multiple field sites to expand the analysis.”
Research into soil biodiversity and health is vital as the agriculture sector works to create agriculture systems that are sustainable by maintaining yields with the least inputs and that also help the environment. The ever-increasing demand on Ontario’s agricultural sector to provide plant biomass in the form of crops for food, animal grain and even biofuels makes this challenging, but producers are interested in trying cover crops and changing microbial communities in soil.
The researchers believe information on soil biodiversity will show the importance of selected management options such as cover crops, reduced tillage and crop rotations in improving soil health and in sustaining crop productivity.
“We understand this is a farm and people need to maintain their yield,”
Dunfield says. “We’re looking for the most sustainable, environmentally ultimate good to achieve that.
“But, right now, there is no tool to measure biological indicators,” she adds. “No one knows what part of biology is important. We need a good way to measure biology in soil and determine what we need there to have healthy soil. We need the research and data to show if a farmer grows this cover crop, this is what it does to the soil.”
Dr. Amanda Diochon, a professor in the Department of Geology at Lakehead University, is part of a multi-partner research study that aims to develop an improved soil health test for Ontario.
The project focuses on how different management practices impact soil health from four Ontario sites – in Ottawa, Delhi, Elora and Ridgetown. For Diochon’s part, she’s tracking how components of organic matter change over time.
“It’s possible for a farmer to optimize fertilizer levels and optimize yield, but that doesn’t necessarily mean soil will be healthy,” Diochon says. “And sometimes yields may be consistent across seasons or crop locations, but soil health in different fields can be variable.”
So if it’s possible to produce a high-yielding crop with less-than ideal soil, why does soil health matter? Diochon says the answer is simple: insurance. Healthy soil will be more productive when conditions are less than ideal.
Healthy soil is more resilient and can deal with stressors brought on by a changing climate. For example, soil with healthy levels of good quality organic matter will hold on to more moisture when climate is dry. And soil with a more diverse and productive microbial community is better able to buffer change.
Diochon is evaluating the effects of crop rotation and tillage on the different properties of organic matter. The key, she says, is in finding indicators in organic matter that are sensitive to change.
“We know what soil health is, but can we measure it? Nobody has that nugget yet,” Diochon says.
Her research team has zoned in on seven key indicators that she says will respond over time. Together, the indicators allow her to measure the physical, biological and chemical properties in soil.
“It’s hard to detect change by measuring organic matter or organic carbon,” Diochon says. “But by looking at certain attributes in organic matter, such as light fraction or sand fraction, we see they are sensitive to change.”
By examining soil samples from four sites in Ontario, Diochon says researchers will have a more comprehensive understanding of how organic matter responds across location and soil type.
“The hope is this research will identify best management practices to maintain or enhance soil health,” Diochon says. “We want to make it as profitable as possible for farmers while minimizing the impact on the environment – and ultimately enhance the resiliency of the entire system.”
This research is funded by the Ontario Ministry of Agriculture, Food and Rural Affairs and Grain Farmers of Ontario.
The first step is the discussion paper called “Sustaining Ontario’s Agricultural Soils: Towards a Shared Vision” now available for comment.
The strategy takes aim at the apparent increasing risk of soil degradation in Ontario and the Ontario Soil and Crop Improvement Association is encouraging farmers to mark Ontario Agriculture Week (Oct. 3-9) in a positive way by contributing commentary on behalf of the farming community. Gord Green, OSCIA president and dairy farmer, says now is the time to voice the perspective of primary producers, not after new policies emerge. But before they do, Green urges farmers to also consider what philosophies they want to see in practice.
“This strategy will lay the basic ground work as to what we should be doing, it’s taking a stand that we can build on in a practical sense,” he explains. “Anyone can and will state good things about the benefits of soil health, but we have to go at it with the right philosophy to truly promote positive change.”
Evidence suggests change in some farming practices may be necessary and Green believes all farmers should consider what might pertain to them. As an example, he offers agri-environmental indicators developed by Agriculture and Agri-Food Canada which estimates 82 per cent of Ontario’s cropland is losing soil organic carbon and 54 per cent now has a high risk of soil erosion above the annual rate of regeneration. Farmers intent on protecting soil health on higher risk sandy and loam soils may need to question their current logic for selecting only annual crops, limited rotations, or varying degrees of tillage.
Paul Smith, senior policy advisor for the Ontario Ministry of Agriculture, Food, and Rural Affairs, emphasizes the need for farmers, farm organizations, governments and other partners to work in collaboration on developing the soil strategy. The discussion paper proposes a draft vision and draft goals and objectives for our agricultural soils and invites comment and asks eight questions for people to respond to. All aspects of soil health and conservation are explored in the paper. How farmers manage soils benefits from having good soil information and mapping for decision making. Having the best advice on soil management for farmers means we need universities and colleges to offer the right types of courses and do research on the right topics. Educational tools like the Environmental Farm Plan and incentives for best management practice adoption also play an important role.
Preliminary discussions have already identified significant challenges for improving soil health in the province. Some Ontario soil resource inventory maps still have not been digitized and digital elevation data and Geographic Information System (GIS) coverage of agricultural land remains limited. Thousands of soil test results, both private and publicly funded, offer a wealth of data for monitoring soil health but a central system for collecting this information has never been developed. Demand continues to grow for a validated on-farm soil health test. Surveys also show a significant decline in soil science program enrollment in both Canada and the United States as emphasis on soil science at universities worldwide continues to decrease. If supported by the industry, possible actions resulting from the development of this strategy could include contemporary updates to information resources, the production of a farm-scale soil health test, and renewal for soil science programs at colleges and universities across the province.
Agriculture minister, Jeff Leal, met with about 30 farmers at Reynolds Bros. Farms in Prince Edward County for a discussion arranged by Mayor Robert Quaiff, to hear firsthand how 60 days without solid rainfall is producing burnt and premature crops forcing them to again seek claims from the province’s insurance program as many did during severe drought conditions in 2012. | READ MORE.
Figure 1. Departure from average precipitation across Ontario from April 1-Sept. 12, 2016 can be viewed here.
If you follow a build-up and maintain approach to fertility and your crop yields are significantly reduced due to growing conditions this year, you may be able to give credit to some of the phosphorus (P) and potassium (K) applied this year to next year’s crops. It’s little solace, surely, but here is how it could work. For example, if you applied P at a rate of 63 lbs/acre P2O5 and K at a rate of 45 lbs/acre K2O to account for crop removal from a 180 bu/acre grain corn crop and only yielded 90 bu/acre, you applied 31.5 and 22.5 lbs/acre P2O5 and K2O, respectively, above actual crop removal. On the other hand, if you harvested grain corn as silage, there may not be a significant difference in nutrient removal. In this case, the best way to know for sure is to submit a whole plant sample for analysis.
Dry soils can also have an impact on soil test results themselves. In a dry year, soils may not replenish easily available pools of nutrients as quickly throughout the season. Even if plant growth and nutrient uptake are less than normal, soil test readings may not reflect this. It may take some time once soil moisture conditions improve in the fall for less easily available pools of nutrients to be converted to forms that are measured by the soil test.
Soil test potassium, in particular, may be affected by dry soil. A lack of soil moisture this season resulted in an increased incidence of K deficiencies (see Figure 2). If fall continues to be dry, it may also take longer for K to leach from crop residues and return to the soil. Also, soil test values for soils low in K may be overestimated, whereas fields high in K may test lower. If you have experienced a very dry season, you may want to delay sampling until a bit later in the fall once you have moist soil conditions for an extended period.
Figure 2. Potassium deficiency in soybean can be viewed here.
Soil pH can also be affected during a dry season. If precipitation has been well below normal, it is possible that applied fertilizer has not have moved down below 6 inches. In these cases, pH may be reported as lower than it actually is. Also bear in mind that if you applied lime in the spring and have received very little rainfall, there may not have been sufficient moisture to fully activate the neutralizing reactions.
When it comes to nitrogen (N), generally speaking, this season did not present a significant risk of N loss from denitrification (saturated soils) or leaching. Therefore, if you anticipate harvesting a much lower corn yield than was fertilized for, there will likely be a substantial quantity of nitrate nitrogen left in the soil. If this is the case, consider seeding a cereal rye cover crop, which is an excellent scavenger of excess nitrogen in the soil profile. The Midwest Cover Crops Council has a very useful online Cover Crop Decision Tool that provides information on seeding rates and timing.
Finally, samples of dry and hard soils can sometimes be difficult to properly collect. If you cannot obtain a proper number of samples (minimum of 20 cores per 25 acres for a standard composite sample) consistently to a six inch depth, your test results will be likely elevated due to nutrient stratification. In this situation, you can try using another type of soil core sampler. Ultimately, if you are not able to sample to the proper depth, consider delaying sampling and using your latest soil test results.
Putting it all together
- Nutrient removal may have been less than normal this season and should be accounted for
- Excess nitrogen may be present as nitrate in the soil if crop yield did not match nitrogen fertilization rate. Consider using a cover crop to capture nitrogen that is vulnerable to being lost over the winter.
- Take caution when interpreting soil sample results acquired in dry soil conditions. Dry conditions may alter values, in particular potassium and pH levels, and may also make it difficult to obtain proper sample depth.
Camberato, J and B Joern. 2012. Nutrient management related to dry soil conditions and poor crop yields. Agronomy Department, Purdue University. https://www.agry.purdue.edu/ext/soilfertility/droughtnutrients.pdf.
Sawyer, J. 2003. Drought impacts on soil fertility management. Department of Agronomy, Iowa State University. http://www.ipm.iastate.edu/ipm/icm/2003/10-6-2003/droughtsoilimpact.html.
Jongeneel, S. 2012. Soil testing after a dry growing season. Department of Crop Sciences, University of Illinois. http://cropsci.illinois.edu/news/soil-testing-after-dry-growing-season.
With funding by Environment and Climate Change Canada through the Lake Simcoe/South-eastern Georgian Bay Clean-Up Fund, SHIP offers financial support for implementing Best Management Practices (BMPs) that improve soil health and reduce edge of field phosphorus loss.
SHIP, which has a similar structure to the Farmland Health Incentive Program, requires producers to complete an on-farm soil health assessment by working with a participating Certified Crop Advisor (CCA). Free of charge to producers, the Soil Health Check-Up and the Muck Soil Health Check-Up offer producers a unique opportunity to develop BMPs that are tailored to the specific needs of their operation.
“This isn’t a one-size-fits-all program," says Christine Schmalz, environmental program manager at OSCIA. "Through working one-on-one with a CCA, producers gain an in-depth understanding of their operation’s Soil Health Challenges and work to develop BMPs that will benefit their farm and the health of the greater watershed.”
The Soil Health Improvement Program offers up to 50 per cent cost-share to a maximum of $20,000 in funding to producers in the Lake Simcoe, Nottawasaga, and South-eastern Georgian Bay watersheds who implement BMPs after completing a Soil Health or Muck Soil Health Check-Up. Eight BMPs are eligible for cost-share under SHIP: cover crops, crop nutrient plans, buffer strips, windbreaks and windstrips, equipment customization, erosion control structures, fragile land retirement, and water runoff management.
This program will begin accepting applications on Sept. 28, 2016 at 12:00 p.m. and funding will be allocated to eligible projects in the order in which applications are received. Producers interested in the program are encouraged to complete their Soil Health Check-Up in preparation. Program materials are now available online as well as a list of participating CCAs who are keen to complete Check-Ups in the eligible area.
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