Crop Sciences

Scientists discover the evolutionary link between protein structure and function

Published May 18, 2016
Heme protein
Heme protein showing loops in orange near the bottom
  • A new University of Illinois study demonstrates the evolution of protein structure and function over 3.8 billion years.
  • Snippets of genetic code, consistent across organisms and time, direct proteins to create “loops,” or active sites that give proteins their function. 
  • The link between structure and function in proteins can be thought of as a type of network.
  • Demonstrating evolution in this small-scale network may help others understand how different types of networks, such as the internet or social networks, change over time.

URBANA, Ill. – Proteins are more than a dietary requirement. This diverse set of molecules powers nearly all of the cellular operations in a living organism. Scientists may know the structure of a protein or its function, but haven’t always been able to link the two.

“The big problem in biology is the question of how a protein does what it does. We think the answer rests in protein evolution,” says University of Illinois professor and bioinformatician Gustavo Caetano-Anollés.

Geologists have found remnants of life preserved in rock billions of years old. In some cases, preservation of microbes and tissues has been so good that microscopic cellular structures that were once associated with specific proteins, can be detected. This geological record gives scientists a hidden connection to the evolutionary history of protein structures over incredibly long time periods. But, until now, it hasn’t always been possible to link function with those structures to know how proteins were behaving in cells billions of years ago, compared with today.

“For the first time, we have traced evolution onto a biological network,” Caetano-Anollés notes.

Caetano-Anollés and graduate students Fayez Aziz and Kelsey Caetano-Anollés used networks to investigate the linkage between protein structure and molecular function. They built a timeline of protein structures spanning 3.8 billion years across the geological record, but needed a way to connect the structures with their functions. To do that, they looked at the genetic makeup of hundreds of organisms.

“It turns out that there are little snippets in our genes that are incredibly conserved over time,” Caetano-Anollés says. “And not just in human genomes. When we look at higher organisms, such as plants, fungi and animals, as well as bacteria, archaea, and viruses, the same snippets are always there. We see them over and over again.”

The research team found that these tiny gene segments tell proteins to produce “loops,” which are the tiniest structural units in a protein. When loops come together, they create active sites, or molecular pockets, which give proteins their function. For example, hemoglobin, the protein that carries oxygen in blood, has two loops which create the active site that binds oxygen. The loops combine to create larger protein structures called domains.

Remarkably, the new study shows that loops have been repeatedly recruited to perform new functions and that the process has been active and ongoing since the beginning of life.

“This recruitment is important for understanding biological diversity,” Caetano-Anollés says.

One important aspect of the study relates to the actual linkage between domain structure and functional loops. The researchers found that this linkage is characterized by an unanticipated property that unfolds in time, an “emergent” property known as hierarchical modularity.

“Loops are cohesive modules, as are domains, proteins, cells, organs, and bodies.” Caetano-Anollés explains. “We are all made of cohesive modules, including our human bodies. That’s hierarchical modularity: the building of small cohesive parts into larger and increasingly complex wholes.”

Hierarchical modularity also exists in manmade networks, such as the internet. For example, each router represents a “node” that pushes information to different computers. When millions of computers interact with each other online, larger and more complex entities emerge. Caetano-Anollés suggests that the evolution of manmade networks could be mapped in the same way as the evolution of biological networks.

“From a computer science point of view, few people have been exploring how to track networks in time. Imagine exploring how the internet grows and changes when new routers are added, are disconnected, or network with each other. It’s a daunting task because there are millions of routers to track and internet communication can be highly dynamic. In our study, we are showcasing how you can do it with a very small network,” Caetano-Anollés explains.

The methods developed by Caetano-Anollés and his team now have the potential to explain how change is capable of structuring systems as varied as the internet, social networks, or the collective of all proteins in an organism.

The article, “The early history and emergence of molecular functions and modular scale-free network behavior,” is published in Scientific Reports. M. Fayez Aziz and Kelsey Caetano-Anollés, also from the University of Illinois, co-authored the report. Full text of the article can be found at: http://www.nature.com/articles/srep25058.

 

     

Mechanism for herbicide resistance in Palmer amaranth identified

Published May 18, 2016
Palmer amaranth
Young Palmer amaranth plant. Photo courtesy of Aaron Hager.
  • Waterhemp and Palmer amaranth are resistant to a class of herbicides known as PPO-inhibitors.
  • The mechanism of resistance is a rare mutation in a genetic sequence not shared by many plants.
  • Researchers who discovered the mutation predict that PPO-resistant Palmer amaranth populations will spread quickly and widely.

URBANA, Ill. – Corn and soybean farmers might as well be soldiers locked in an ever-escalating war against the weeds that threaten their crops. New weapons—herbicides—only work for so long before the enemy retaliates by developing resistance and refusing to die. So farmers attack with new herbicides or new mixtures of existing herbicides until the cycle starts again. This has been the case for decades for two familiar enemies, waterhemp and its aggressive cousin, Palmer amaranth.

A new study co-authored by University of Illinois weed scientist Patrick Tranel shows that Palmer amaranth populations from Arkansas are now resistant to a class of herbicides known as PPO-inhibitors (PPOs).

PPOs were used extensively in the early 1990s in soybeans after waterhemp developed resistance to the class of herbicides known as ALS-inhibitors. But when Roundup Ready® crops came along, most farmers switched to using glyphosate, with PPOs applied to soil prior to weed emergence. Thus, when glyphosate stopped working on waterhemp and farmers went back to PPOs for post-emergence control, they were surprised to find that they no longer worked on waterhemp in some fields.

“The PPOs applied pre-emergence were providing selection pressure and increasing the resistance to PPOs without farmers really knowing about it. That’s one of the reasons we think we have so much PPO resistance now,” Tranel explains. 

But PPO resistance in waterhemp is old news. What’s interesting is the mechanism of resistance to PPOs.

The genetic code of an organism, which determines all of its physical traits, is housed in its DNA in molecules known as nucleotides. Normally, mutations in genetic sequences that give rise to herbicide resistance happen at the scale of a single nucleotide.

In PPO-resistant waterhemp, however, Tranel’s group found a different mutation. Instead of a change in a single nucleotide, they found the deletion of three nucleotides. “It seems like it would be really rare and difficult for this particular mutation to occur. It just shouldn’t happen,” Tranel says. But, for waterhemp, it did.

This mutation probably happened because the sequence of three nucleotides was repeated, and this repeat just happened to be in the right place in waterhemp’s genetic code.

So the team looked at the genetic sequences of related pigweeds, to see if they had the repeat in the right place, and found that most did not. However, when they looked at the genetic code for Palmer amaranth, they found the repeat. They predicted that, someday, they’d see Palmer amaranth developing resistance to PPOs.

“Palmer has this repeat. It’s predisposed to PPO resistance. If waterhemp can do it, Palmer can too,” Tranel notes.

Soon, several of Tranel’s colleagues started hearing reports from farmers about Palmer amaranth that wasn’t being killed by PPOs. When Tranel tested samples sent from Arkansas and Tennessee, he found the mutation. His prediction had been right.

“We predict PPO resistance is going to spread very rapidly in Palmer, like it did in waterhemp. By now, we know PPO-resistant Palmer is present in at least three states. If a farmer has Palmer, they should not rely on PPO as an effective herbicide. It might only work for a couple of years,” Tranel says.

In fact, when Tranel and his colleagues tested the effectiveness of the PPO inhibitor fomesafen on an Arkansas population of Palmer amaranth, they found that each successive generation had a higher frequency of the mutation and required more and more PPO to be applied to achieve a 50 percent growth reduction.

The rapid spread of the mutation in these populations is bad news for farmers, but intriguing from an evolutionary science point of view.

“That’s why resistance is so cool: it’s just evolution,” Tranel says. “We can study it at warp speed. Most people who study evolution have to deal with time scales of hundreds or thousands of years. We can study evolution in five or ten years.”

How can farmers deal with this new threat? Tranel says they should “pray for a new herbicide.”

But for the time being, he suggests they use as many different pre- and post-emergence herbicides with as many modes of action as possible in every field in every year.

The battle continues.

The article, “Resistance to PPO-inhibiting herbicide in Palmer amaranth from Arkansas” is published in Pest Management Science. The research was supported by the Arkansas Soybean Research and Promotion Board, Cotton Incorporated, and Syngenta Crop Protection.

The full text of the article is available at http://onlinelibrary.wiley.com/doi/10.1002/ps.4241/full.

Cancer-fighting properties of horseradish revealed

Published May 17, 2016
horseradish root
Horseradish plant
  • Horseradish contains cancer-fighting compounds known as glucosinolates.
  • Glucosinolate type and quantity vary depending on size and quality of the horseradish root.
  • For the first time, the activation of cancer-fighting enzymes by glucosinolate products in horseradish has been documented.

URBANA, Ill. – The humble horseradish may not be much to look at, but a recent University of Illinois study shows that it contains compounds that could help detoxify and eliminate cancer-causing free-radicals in the body.

“We knew horseradish had health benefits, but in this study, we were able to link it to the activation of certain detoxifying enzymes for the first time,” says U of I crop scientist Mosbah Kushad.

Kushad’s research team had previously identified and quantified the compounds responsible for the cancer-fighting compounds, known as glucosinolates, in horseradish, noting that horseradish contains approximately 10 times more glucosinolates than its superfood cousin, broccoli.  

“No one is going to eat a pound of horseradish,” Kushad points out. Luckily, a teaspoon of the pungent condiment is sufficient to get the benefit.

In the new study, Kushad and his team looked for the products of glucosinolate hydrolysis, which activate enzymes involved in detoxification of cancer-causing molecules. They compared the quantity and activity of these products in 11 horseradish strains rated U.S. Fancy, U.S. No. 1, or U.S. No. 2. The USDA puts fresh-market horseradish in these categories based on diameter and length of the root.

“There was no information on whether the USDA grade of the horseradish root is associated with cancer preventive activity, so we wanted to test that,” Kushad explains.

The group found that the higher-grade U.S. Fancy accessions had significantly more glucosinolates than U.S. No. 1. Concentrations of various glucosinolate hydrolysis products differed according to USDA grade, with U.S. Fancy having greater allyl isothiocyanate (AITC) and U.S. No. 1 having greater 1-cyano 2,3-epithiopropane (CETP).

The two compounds differ, with CETP being a comparatively weaker cancer-fighter than AITC. Still, the detection of CETP in horseradish is noteworthy, according to Kushad. “To our knowledge, this is the first detection and measurement of CETP from horseradish,” he says.

The team suggests that AITC is a good dietary anti-carcinogen, not only because it activates the enzyme responsible for detoxifying cancer-causing molecules, but also because a large proportion of it, 90 percent, is absorbed when ingested.

Bottom line? Next time horseradish is on the menu, pick up a spoon.

The article, “Correlation of quinone reductase activity and allyl isothiocyanate formation among different genotypes and grades of horseradish roots,” appears in the Journal of Agricultural and Food Chemistry, and online at http://pubs.acs.org/doi/abs/10.1021/jf505591z. Co-authors K-M Ku, E.H. Jeffery, and Jack Juvik are also researchers at the U of I.

Challenges of springtime weeds

Published May 12, 2016
yellow rocket and butterweed

URBANA, Ill. – The springtime color scheme provided by winter annual weed species in many no-till fields has shifted from the hearty purple of flowering henbit and purple deadnettle to the bright yellow flowers of two species. Yellow rocket and cressleaf groundsel (a.k.a. butterweed) both produce bright yellow flowers and are common across much of the southern half of Illinois. 

University of Illinois weed scientist Aaron Hager explains the difference between butterweed (Packera glabella) and yellow rocket (Barbarea vulgaris), both winter annual species.

“Most of the yellow-flowered plants currently in fields are butterweed, which is in the same plant family as daisies. The flowers are bright yellow and grouped in clusters on several flowering stalks of the plant. Seeds are easily dispersed via wind due to the fluffy white hairs that catch the breeze,” he says.

Yellow rocket is a winter annual species in the mustard plant family. Flowers are produced on spike-like stalks and consist of four petals that form a cross. Seed pods are about 1 inch long and nearly square in cross section.

Hager points out that because plants are at the flowering stage in many fields, farmers should not skimp on burndown herbicides to control seed spread.

“The yellow flowers mean the plants are close to completing their lifecycle, and their sheer size will make them more challenging to control compared to when the plants were still in the vegetative stages. Complete control is important to reduce seed production which will be helpful for many future seasons,” Hager says.

Butterweed and yellow rocket are not the only weeds farmers must contend with now. Marestail (Conyza canadensis), also in the daisy family, produces small white flowers and numerous tufted seeds at maturity. Farmers know it as one of the most challenging weeds to control prior to planting no-till soybean. 

“Already this season, some have reported poor marestail control following applications of glyphosate plus 2,4-D. Poor control can be caused by several factors, including large plant size and resistance to glyphosate,” Hager explains. 

Hager says to avoid relying solely on 2,4-D for glyphosate-resistant marestail.

“Adding Sharpen or metribuzin to glyphosate plus 2,4-D can improve marestail control. Include MSO with Sharpen and be sure to adhere to planting intervals in treated fields where another soil-applied PPO inhibitor will be used. Glufosinate (Liberty, Interline, etc.) or Gramoxone SL are other options to control marestail before planting,” Hager says. 

Control is often improved when these products are tank-mixed with metribuzin and 2,4-D.  Both glufosinate and Gramoxone are contact herbicides, so Hager suggests adjusting application equipment (nozzles, spray volume, etc.) to ensure thorough spray coverage.

Another option to control emerged marestail is tillage. Hager says farmers should delay tillage until field conditions are suitable and till deep enough to completely uproot all existing vegetation.

More information on the biology and control of these spring weeds can be found at http://bulletin.ipm.illinois.edu/?p=3589 and http://bulletin.ipm.illinois.edu/?p=3584.

News Source:

Aaron Hager, 217-333-4424

Data-intensive farm management program receives $2.4 million grant, seeks participants

Published May 10, 2016
aerial view of farm fields
Aerial view of farm fields

URBANA, Ill. – The USDA National Institute of Food and Agriculture recently announced a $2.4 million grant through its Agriculture and Food Research Initiative to fund an interdisciplinary program led by researchers at the University of Illinois. The data-intensive farm management (DIFM) program will use precision agriculture technologies to run full-field, on-farm agronomic trials that change application rates of nitrogen fertilizer. The data generated from the project will help farmers manage nitrogen application to increase profits and reduce nutrient runoff.

Until now, precision agriculture technology’s potential for improving farm management has not yet been fully realized.

“What we’re doing differently is changing the management variables,” says U of I agricultural economist David Bullock. “We’re characterizing the fields and taking yield data, but we’re also going to be changing nitrogen application rates on a fine scale throughout each field. This will generate a lot of information on what works and what doesn’t.”

The team of 28 researchers and extension personnel from six universities will be coordinating on-farm experiments across 100 fields in Illinois, Nebraska, Kentucky, Argentina, and Uruguay over the four-year study period. In addition to generating a substantial amount of data, the ultimate aim of the project is to develop software that will communicate management ideas to farm advisors. Once that software is developed, the researchers hope to run trials on thousands of farms.

“Because all our experiments will be run on a common framework, we will end up with a lot of data,” Bullock reports. “We’re going to use cutting-edge statistical and economic analysis to determine how different farm characteristics affect optimal application rates.”

Existing management recommendations are often geared toward entire regions or cropping systems, without taking site-specific data into account. The researchers estimate that, after a few years, they will be able to give farmers profitable advice based on experimentation done in their specific fields.

“That’s revolutionary,” says Bullock.

The researchers are seeking farmers to participate in the study. Although farms will become experimental sites, disruption to farmers will be minimal. Experimental protocols will be automatically programmed into farm machinery, meaning farmers simply need to drive their machines as usual. Importantly, farmers will be fully compensated for any losses throughout the experimental period. They will also receive $500 for their participation in the project. 

Interested parties can email David Bullock (dsbulloc@illinois.edu) or Don Bullock (dbullock@illinois.edu) for more information and to sign up.

-30-

Spring nitrogen management for corn

Published April 27, 2016
Corn

URBANA, Ill. – Although the price of nitrogen fertilizer has fallen in the past year, the lower price of corn means that decisions about nitrogen management need to be made carefully, with an eye towards maximizing the return on investment for this important input.

The first question on nitrogen management is rate: How much nitrogen will the crop need, and how much of this will need to come from fertilizer?

“The generally accepted rule of thumb is that the crop will take up a total of about one pound of nitrogen for each bushel of yield. We’ve found a similar number in a few studies we’ve done,” says University of Illinois crop scientist Emerson Nafziger.

Not all of the nitrogen needed for the crop has to come from fertilizer, though; some of it will come from soil organic matter. How much the soil provides is related to soil depth and amount of organic matter, but it also varies by year, depending on weather and crop conditions. That makes the amount difficult to predict.

“In the deeper, higher organic matter soils in Illinois, we might see amounts of up to 200 pounds of nitrogen per acre available to the crop in a good year, while in shallower and lower organic-matter soils or in a year with cool, dry soil conditions this could be as little as 20 or 30 pounds,” Nafziger notes.

At current corn and nitrogen prices, studies over recent years have shown that corn following soybean in southern and central Illinois should be fertilized with about 175 pounds of nitrogen per acre, while in northern Illinois, where more nitrogen is present in the soil, this rate is about 150 pounds of nitrogen. For corn following corn, the rate that provides the maximum return to nitrogen is about 200 pounds of nitrogen per acre everywhere, but perhaps slightly less in southern Illinois.

Form, timing, and placement of nitrogen fertilizer can affect nitrogen availability to the crop.

“Knowing the basics of how different fertilizer materials behave can only take us so far,” Nafziger says. “What happens to nitrogen in the soil that affects it availability to the crop is heavily dependent on weather. This means that our predictions regarding nitrogen form and timing are only about as good as our ability to predict the weather before the season starts.”

Still, nitrogen management can be improved with research over a range of sites and years. Nafziger and his research team initiated a large study in 2014 to look at the effect of nitrogen form, timing, and placement on corn yield. There were a total of 15 treatment variables in the study, but the nitrogen application rate was held constant at 150 pounds per acre.

Yield varied somewhat with the form of nitrogen applied. Dry forms of urea with Agrotain® and SuperU® applied at planting produced the highest yields, but yields obtained with urea ammonium nitrate (UAN) injected at planting and of anhydrous ammonia with N-Serve were also high.

The team also experimented with non-traditional application methods and timing, such as surface-banding UAN at planting and holding some of the nitrogen back until tasseling. 

“While we saw some small differences among treatments, commonly used timing and forms of nitrogen all produced similar yields, even under what we would consider high-loss conditions with all the rain in June 2015,” Nafziger says.

Their results showed that both the risk of nitrogen loss and the benefit from delaying nitrogen application or using inhibitors were less substantial than expected.

“That provides some confidence that most of the nitrogen management systems in use today have good potential to provide the crop with adequate nitrogen. Adding costs by changing nitrogen management, for example by making another trip over the field to apply late nitrogen, may not provide a positive return compared to applying all of the nitrogen in one or two earlier trips,” Nafziger says.

Nafziger’s research is sponsored by the Nutrient Research and Education Council. More details and data can be found at http://bulletin.ipm.illinois.edu/?p=3561.

Planting date: Corn or soybean first?

Published April 26, 2016
corn seedlings

URBANA, Ill. – Many Illinois corn and soybean growers are busy planting their crops, with 42 percent of the corn and two percent of the soybean crop planted as of April 24. However, those producers who are just getting started or are still waiting for dry fields may not see a large yield penalty, according to University of Illinois crop scientist Emerson Nafziger.

“We’ve run 35 corn planting-date trials in central and northern Illinois over the past nine years, with four planting dates at each site beginning in early April and going through late May or early June,” Nafziger says.

Nafziger’s data indicated the planting date that gave the highest corn yield was April 17, but that date was not substantially different compared to April as a whole. For example, yields were within 1 percentage point (about 2 bushels per acre) of the maximum between April 5 and April 30.

“Beyond April, we predict yield losses of about 4 percent (8 bushels per acre) by May 10, 8 percent (17 bushels) by May 20, and 14 percent (29 bushels) if planting is delayed until May 30,” Nafziger states. “We don’t have a lot of data for June planting, but the yield loss going into June is at about 2 bushels per day of delay, and it’s accelerating.”

Nafziger’s research team has also gathered 23 site-years of planting-date data for soybeans in the same sites as their corn studies. The earliest planting date for soybeans was in the second week in April, with the latest dates in mid-June.

The data for soybeans showed that the maximum yield was obtained in mid-April, and that yield loss by the end of April was about 4 percentage points, or about 2.5 bushels. After April, losses totaled 7 percent (4 bushels per acre) by May 10; 10 percent (7 bushels) by May 20; 16 percent (11 bushels) by May 30; 21 percent (14 bushels) by June 10; and 29 percent (19 bushels) if planting was delayed to June 20.

“On a percentage basis, these loss numbers are slightly greater than those from planting delays in corn, but some of this is due to planting soybeans a little later in April than we started planting corn. Both crops lost yield at about the same rate as planting was delayed into late May,” Nafziger notes. “That runs counter to the earlier findings that corn loses yield faster when planting is delayed, and therefore needs to be planted earlier.”

Given that neither crop suffers dramatically from planting through early May, farmers might assume that planting priorities for both crops are similar. But because corn seedlings tend to emerge better than soybeans under soil conditions typical of early spring, Nafziger still suggests starting with corn, at least until soils warm up, to allow faster soybean emergence.

“While letting both crops planted on time is beneficial, we shouldn’t lose sight of the fact that yield losses for delays into and even past mid-May are not so large that we need to give up hopes for a good crop if we aren’t done planting by the end of April,” Nafziger says.

More details and data from field studies are available at: http://bulletin.ipm.illinois.edu/?p=3564

Bioreactors ready for the big time

Published April 26, 2016
Bioreactor construction
Bioreactor construction on a dairy farm. Photo courtesy of Brandon C. Goeller, University of Canterbury, New Zealand.
  • Bioreactors are passive filtration systems that can reduce nitrate losses from farm fields.
  • Most bioreactors are simple pits filled with wood chips; bacteria on the wood chips remove 25 to 45 percent of the nitrate in runoff water.
  • Research summarized in a special issue of the Journal of Environmental Quality highlights their potential applications and provides insight into design options.

URBANA, Ill. – Last summer, the Gulf of Mexico’s “dead zone” spanned more than 6,400 square miles, more than three times the size it should have been, according to the Gulf Hypoxia Task Force. Nitrogen runoff from farms along the Mississippi River winds up in the Gulf, feeding algae but depriving other marine life of oxygen when the algae decomposes. The 12 states that border the Mississippi have been mandated to develop nutrient reduction strategies, but one especially effective strategy has not been adopted widely: bioreactors.

Bioreactors are passive filtration systems that capitalize on a bacterial process known as denitrification to remove from 25 to 45 percent of the nitrate in water draining from farm fields. Research on and installation of bioreactors has accelerated in the past decade, but University of Illinois assistant professor of water quality Laura Christianson and her colleagues are urging a move past proof-of-concept toward large-scale deployment.

“Bioreactors are one of the most effective edge-of-field practices, but until now, they haven’t been rolled out on a large scale,” Christianson says.

Designs vary, but the typical arrangement for a 40- to 80-acre field is a large (100 x 20 foot) pit situated just ahead of where drainage pipes flow into ditches or streams. The pit is filled with carbon-rich organic material: usually wood chips, but sometimes corn cobs, biochar, or other matter. Denitrifying bacteria make their homes in the organic material and utilize its carbon as an energy source to convert nitrate in the water to the harmless nitrogen gas that makes up 78 percent of our atmosphere. 

A benefit of bioreactors as a nitrogen management strategy is their cost-benefit ratio. Bioreactors can cost approximately $10,000 to install, but cost-sharing is available through the USDA’s Natural Resources Conservation Service for approximately half of that. Importantly, bioreactors typically operate for 10 years before wood chips need to be replaced.

“It’s a big up-front cost compared to a cover crop, but then you’re ‘one and done’ for 10 years,” Christianson notes.

Christianson put together a special issue of the Journal of Environmental Quality focusing on bioreactors. Fifteen articles in the issue summarize the state-of-the-art of bioreactor technology, confirming that bioreactors could be an effective part of an integrated approach to nitrate management.

A large component to bioreactor efficiency is design.

According to Christianson and other experts contributing to the special issue, flow rates can significantly affect the efficiency of bioreactors. During low-flow periods, water can be held in bioreactors for too long, setting up conditions for different bacteria that create noxious hydrogen sulfide gas. Likewise, in high-flow periods, water may move through too quickly for efficient nitrogen removal.

“Tile drainage systems never flow at a consistent rate,” Christianson explains. “Bioreactors have to be designed strategically to optimize retention time and maximize nitrate removal without undesirable byproducts.”   

Temperature and seasonal changes also affect how well bioreactors work.

“The critical period for nitrate loss is early spring, before plants are growing and taking up nitrogen,” Christianson says. “Snowmelt puts a significant amount of water through a bioreactor, depending on where you are. And because snowmelt and early spring drainage water is cooler, the bacteria aren’t as efficient.”  

Christianson and her colleagues are calling for more field-scale research to optimize design for the set of conditions unique to each field.

“That’s where my interest is for research: coming up with better designs. But on the other side of that coin, we don’t want to become so advanced in the design that it becomes really complicated. There’s a beauty in the simplicity of a trench full of woodchips,” Christianson says.

The article introducing the special issue, “Moving denitrifying bioreactors beyond proof of concept: Introduction to the special section,” appears in the Journal of Environmental Quality along with 14 additional articles on the topic. Christianson co-authored the introductory article with Louis Schipper of the University of Waikato in New Zealand.

Links to the articles, several of which can be read in full without a subscription, can be found at: https://dl.sciencesocieties.org/publications/jeq/tocs/45/3#h1-SPECIAL%20SECTION:%20MOVING%20DENITRIFYING%20BIOREACTORS%20BEYOND%20PROOF%20OF%20CONCEPT

 

Herbicide resistance in waterhemp continues to grow

Published April 20, 2016
Hager with waterhemp
Hager with waterhemp
  • Populations of the broadleaf weed waterhemp have been found to be resistant to the class of herbicides known as HPPD-inhibitors.
  • A University of Illinois study shows waterhemp resistant to HPPD-inhibitors were also resistant to several other classes of herbicides, making it even harder to control chemically.
  • Weed management programs that do not rely exclusively on chemical methods may be the key to reducing waterhemp populations over time.

URBANA, Ill. – Twenty-five years ago, waterhemp was virtually unknown to Illinois farmers. Today, the broadleaf weed blankets corn and soybean fields across the state and the Midwest, causing yield losses from 40 to 70 percent.

As it marched through the region, waterhemp began to develop resistance to the most commonly used herbicides of the day. A relatively new type of resistance to a class of herbicides called HPPD-inhibitors was discovered in waterhemp populations in Illinois and Iowa in 2009. Now, thanks to a new University of Illinois study, we know that some of those populations are also resistant to alternative herbicides, making them even harder to kill.

“We looked at the response of a McLean County, Illinois, population to a number of HPPD-inhibitors and several herbicides of six other classes in the field and in the greenhouse,” says University of Illinois weed scientist Aaron Hager.

The researchers looked at whether it was possible to control plants with higher application rates of HPPD-inhibitors. But it turned out that, even with twice the label rate of some HPPD-inhibitors, the plants were able to recover after two weeks.

“When we did our first greenhouse work with this, no one had ever seen this kind of recovery before. When we looked at the plants seven days after spraying with HPPD-inhibitors, they were very injured. But, by 12-14 days, you could see that new, healthy tissue was emerging from the plants,” Hager recalls.

The researchers also evaluated the timing of post-emergence herbicide application.

“The idea was that perhaps a smaller plant size might be more sensitive than a larger plant,” Hager explains. “The level of injury of small, 1- to 2-inch plants was more than what we recorded on larger plants, but it was still less than an acceptable level of control. So, really, application timing is not going to be something that a farmer could use to overcome HPPD-resistance.”

When waterhemp was treated with herbicides from different classes, there was more bad news.

“We essentially confirmed that we can’t control this population with three classes of herbicides, the HPPD-inhibitors, the ALS-inhibitors, or the PSII-inhibitors. The weight of everything together points to the fact that this population is using resistance mechanisms that we haven’t seen before,” Hager says.

That said, the McLean County population is not the only waterhemp population that is resistant to multiple herbicide classes. In fact, Hager says that it’s rare to find a population that is resistant to only one class.

“What’s changed over time is the number of different classes to which it’s resistant. In 2000, we first found a population that had three-way resistance. Then we found one with four-way resistance. Those are individual plants with resistance to two, three, or four different classes of herbicides,” Hager notes.

There are some herbicides that are still effective, at least on specific populations. The McLean County population is sensitive to glyphosate, glufosinate (a GS-inhibitor), and multiple PPO-inhibitors, such as fomesafen.

Hager cautions that, with certain resistance mechanisms, the ability to predict which herbicides will be effective on any given population has been lost, and that chemical control alone is not the answer. If a farmer switches to a class of herbicides that works today, it is unlikely to work for very long before waterhemp develops resistance.

“Ultimately, we know how to win the battle,” Hager says. “If we attack waterhemp at the most vulnerable stage in its life cycle—the seed—we could beat this thing in five to seven years.”

Hager recommends that farmers let seeds germinate, then mechanically work the soil before planting the crop.

“You’ve just reduced your seedbank by millions, maybe hundreds of millions, and it didn’t cost you a dime,” Hager notes.

Farmers should repeat this strategy for multiple years until the seedbank is diminished. Another key is pulling out any stragglers before they go to seed.

“Let’s say it’s late July, and you see a few of these things popping up. Don’t let them go to seed,” Hager warns. “It’s not fun. At that time of year, it’s hot, sticky, and miserable, but the ultimate goal is to reduce the seedbank. You can’t let female plants go and make hundreds of thousands of seeds and then run a combine through at the end of the year. You’re going to reseed that whole field.”

According to Hager, no new herbicides are being developed that are likely to work on waterhemp long-term.

“We’ve got to get people off this idea that we’ve got a chemical solution for waterhemp, because in some cases, we don’t,” Hager adds.

The article, “Responses of a waterhemp (Amaranthus tuberculatus) population resistant to HPPD-inhibiting herbicides to foliar-applied herbicides,” is published in Weed Technology. Lead author, Nicholas Hausman, along with co-authors Patrick Tranel, Dean Riechers, and Hager, are from the University of Illinois. Financial support was provided by Syngenta Crop Protection.

The paper can be read at http://www.wssajournals.org/doi/full/10.1614/WT-D-15-00098.1.

Plan to attend U of I Agronomy Day 2016 in its new location

Published April 19, 2016
corn

URBANA, Ill. – Mark your calendars for an opportunity to explore the latest research in crop sciences during the 59th annual Agronomy Day at the University of Illinois on August 18.

"Agronomic research has been conducted at the University of Illinois since the university’s earliest days," says Bob Dunker, agronomist and former superintendent of the Crop Sciences Research and Education Center and chairperson for Agronomy Day. “The first Agronomy Day held in 1957 had the same objective as the one you will attend this year—to communicate research results that benefit the agriculture community, which in turn helps feed our growing population across the globe.”

Importantly, Agronomy Day will be held in a new location this year. The Crop Sciences Research and Education Center South First Street Facility, located at 4202 South 1st Street in Savoy, will provide more parking, space for laboratory tours, shorter tour walking distances, and less traffic from campus. Directions to the new facility appear on the Agronomy Day website.

Nearly 1,000 visitors are expected to attend Agronomy Day. Researchers will discuss a variety of topics from soil fertility to insect management, crop production, weed control, corn and soybean genetics, plant diseases, farm economics, and agricultural engineering.

Field tours depart at 7 a.m. from the main tent at the new location, making stops at research plots continuously until 2 p.m. Lunch is available for a nominal charge. The exhibition tent will feature exhibits by ACES programs, commercial vendors, research posters, and student clubs.

More information and registration can be found at http://agronomyday.cropsci.illinois.edu/ or by contacting Sue Overmyer at 217-300-3702 or overmyer@illinois.edu.

News Source:

Bob Dunker, 217-244-5444

Pages