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Environmental DNA provides early detection of invasive crayfish

Published September 20, 2016
Eric Larson, U of I aquatic ecologist
Eric Larson, U of I aquatic ecologist
  • Ecosystems contain environmental DNA (eDNA) that includes genetic information on every organism within them.
  • By analyzing eDNA from 12 Wisconsin lakes, researchers determined the presence of an invasive crayfish species, including in two lakes that had never reported this crayfish.
  • Early detection of invasive species is critical for time-sensitive and cost-effective management responses like containment or removal.

URBANA, Ill. – Every plant and animal has a unique genetic composition, which makes a lake like a bowl of DNA soup—every spoonful contains the combined DNA of the lake’s inhabitants. Scientists have only recently begun using this environmental DNA, or eDNA, to identify the presence of organisms like amphibians and fish. A U of I researcher and his colleagues analyzed eDNA to successfully detect the presence of the highly invasive rusty crayfish in a dozen Wisconsin lakes. Using eDNA to monitor hard to detect species can provide early warnings of newly arrived invasive species.

“The lakes in the Boulder Junction area have had long-term monitoring from the University of Wisconsin and the University of Notre Dame, so we had an existing gradient of lakes where this invasive crayfish had never been observed to lakes where we know rusty crayfish are abundant,” says U of I aquatic ecologist Eric Larson. “Using the eDNA tool we succeeded in detecting rusty crayfish in lakes where this species is very rare. This suggests that the tool could be used to monitor for early warning of new invasions in other regions, which would let us enact control or eradication measures when they’re most feasible.”

Larson says he was skeptical of using eDNA for this particular species. The tool has been successful in finding fish and amphibians which are very mobile, more mucousy, and, presumably, constantly shedding DNA into the environment. “With my background as a field biologist, I thought—Crayfish. With an exoskeleton. Under a rock. At the bottom of a lake. I didn’t think we’d find any using this environmental DNA approach. Obviously, I’m a convert.”

In the study, samples were analyzed using a small white machine that could be easily mistaken for a bread maker. Inside, a computer with a laser heats and cools the samples of DNA over and over in a chemical solution. During each cycle, the double strands of DNA are separated, then built up again. The duplication is exponential so millions of copies are created within a very short time. Beforehand, a dye is attached to the DNA, making it easier for researchers to identify each organism’s DNA and quantify it.

Larson’s colleague Mark Davis, coordinator of the Collaborative Ecological Genetics Laboratory at the Illinois Natural History Survey, explains that every living thing is constantly sloughing off cells and all of those cells contain DNA. But eDNA isn’t like what you get if you take a blood sample from a salamander. That would be “clean DNA.” You already know it’s from a salamander.

“The eDNA from a lake is ‘dirty’ DNA,” Davis says. “It’s degraded, broken down so you have very small fragments and few copies. With chemistry and technology, we amplify it. Using bioinformatics, the computer wades through the information to give us a full complex of what’s in that sample—whether it be invertebrates, fish, reptiles, amphibians, birds—anything that may be coming into contact with the water or soil. With eDNA, it’s exciting because you don’t know what you’ll find.”

Davis says there are still eDNA problems to solve. “Right now we can tell if an organism is present or not. But knowing the exact number of individuals is difficult. For example, we often don’t know the rate an organism sheds DNA or if they shed more at different times. How quickly does it degrade?”

Larson says that one potential disadvantage to using this hypersensitive tool is that it may increase the potential for finding false positives, or cases where an organism is perceived as present when it’s not. This can occur if field or laboratory equipment is contaminated or if DNA is transported long distances via predators or water currents. In the case of Larson’s study, crayfish eDNA was detected in two lakes where the invader had not previously been observed by more conventional methods. Larson says that a minute amount of DNA could have been transported in feces from birds that had fed on crayfish in a different lake, as one example of potential error associated with eDNA.

“It may be that these are new or incipient invasions that eDNA detected before other methods. But it may also be that we had false positives. As a consequence, these are lakes that we want to monitor and follow-up on,” he says.

Globally, there are around 600 crayfish species, of which only about a half dozen have become problematic invaders in the United States. These non-native crayfish prey on fish eggs and destroy aquatic plants, and can negatively affect fish through competition for food and changes to their habitat.

“There are economic repercussions from invasions,” Larson says. “One eradication of rusty crayfish in Wisconsin took years and was very costly.” In that instance, success may have been due to a drought that substantially lowered the lake levels and stranded their habitat.

“Crayfish can walk over land so if you have them in an aquaculture pond there’s nothing to prevent them from crossing over a little hill and then showing up in a national park,” Larson says. “They’re also prevalent in elementary and middle school science classrooms as live animals for behavioral studies. Teachers may not want to euthanize the crayfish at the end of the school year. Often believing that there is just one crayfish species everywhere, they have an end-of-semester release party and dump aquarium contents into a local pond or stream, or send crayfish home with students who may subsequently release them.”

Larson says preventing invasions from happening in the first place is ideal. “But the eDNA tool gives us a sensitive and potentially affordable method for monitoring hard to detect species for management applications. That can mean early warnings of these species invasions while you still have the time to control or contain them before they are too abundant for that to be feasible.”

“Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances,” is published in the Journal of Applied Ecology. The article is co-authored by Eric R. Larson, U of I; Matthew M. Dougherty, Mark A. Renshaw, Crysta A. Gantz, Daniel M. Erickson, and David M. Lodge, all from the University of Notre Dame; and Scott P. Egan, Rice University. The research was supported by a USA EPA grant.

 

High resolution images are available for this story at https://www.youtube.com/watch?v=jbiDfaAzWhA
Sep29

Webinar: Packaging Techniques to Improve Soy Food Shelf Life

11:00 AM - 12:00 PM
Webinar

This webinar, Packaging Techniques to Improve Soy Food Shelf Life, will focus on the range of packaging techniques for soy dairy products and the best practices for each to ensure greater success and financial growth of soy dairy enterprises.  The webinar will review technical information regarding different packaging and distribution options including the use of glass versus plastic bottles, different refrigeration options, bottle sealing, pasteurization, and same day distribution scenarios. Case studies from the Soybean Innovation Lab’s soy dairy network will provide real world examples of these techniques in action. 

Click here for more information and to register.

Anticipating changes in corn and soybean production forecasts

Published September 19, 2016

URBANA, Ill. – Following the release of the USDA’s September Crop Production report, market discussion immediately turned to the likely size of the final corn and soybean production estimates to be released in January. According to a University of Illinois agricultural economist, those estimates will reflect possible changes in both yield and acreage estimates.

Darrel Good provides a historical perspective that may help in anticipating changes this year.

“For corn, the Sept. 12 Crop Production report forecast a crop of 15.903 billion bushels, reflecting an average yield of 174.4 bushels on harvested acreage of 86.55 million acres,” Good says. “The yield and production forecasts are slightly smaller than the August forecasts and the acreage estimate is based on the USDA’s June Agricultural Survey. In the previous 20 years, the U.S. average corn yield estimate released in January after harvest exceeded the September forecast 14 times and was less than the September forecast six times.”

Good says the January estimate exceeded the September forecast 70 percent of the time regardless of whether the September forecast was above (10 years) or below (10 years) the August forecast.

“If the analysis is extended to the previous 40 years, the January corn yield estimate exceeded the September forecast 68 percent of the time, 27 years,” Good says. “However, the January estimate exceeded the September forecast 80 percent of the time when the September forecast equaled or exceeded the August forecast (20 years), and only 55 percent of the time when the September forecast was smaller than the August forecast (20 years), as was the case this year.”

For soybeans, Good says the September report forecast a crop of 4.201 billion bushels, reflecting an average yield of 50.6 bushels on harvested acreage of 83.037 million acres. The yield and production forecasts are larger than the August forecasts and the acreage estimate is based on the USDA’s June Agricultural Survey. In the previous 20 years, the U.S. average soybean yield estimate released in January after harvest exceeded the September forecast 11 times and was less than the September forecast nine times. The January estimate exceeded the September forecast 67 percent of the time when the September forecast was above the August forecast (nine times), as was the case this year, but only 55 percent of the time when the September forecast was below the August forecast (11 years).

“If the analysis is extended to the previous 40 years, the January soybean yield estimate exceeded the September forecast 58 percent of the time (23 years),” Good says. “However, the January estimate exceeded the September forecast 65 percent of the time when the September forecast exceeded the August forecast (20 years) and 50 percent of the time when the September forecast was smaller than the August forecast (20 years).”

In the case of acreage, the USDA’s National Agricultural Statistical Service (NASS) final estimate of planted and harvested acreage will be based on the December Agricultural Survey as well as administrative data, primarily planted acreage reported to the USDA’s Farm Service Agency (FSA) by producers participating in commodity programs. Those administrative data are used by NASS beginning with the October Crop Production report.

“Because the FSA acreage data are used to supplement the NASS survey estimates, there has been a consistent relationship between the final NASS planted acreage estimates and the final FSA acreage estimates,” Good says. “Because all farms do not participate in farm programs, final NASS planted acreage estimates exceed acreage reported to FSA. In the nine years from 2007 through 2015, the NASS planted acreage estimates for corn exceeded acreage reported to FSA by an average of 3.4 percent, in a range of 2.6 to 4.7 percent. The difference was between 3.0 and 3.5 percent in seven of the nine years. For soybeans, the NASS planted acreage estimates exceeded acreage reported to FSA by an average of 1.8 percent, in a range of 1.2 to 3 percent.”

The FSA releases monthly summaries of cumulative producer acreage reports beginning in August and concluding in January. “The September report this year showed very small increases in corn and soybean acreage compared to the August report,” Good says. “This suggests that acreage reporting is occurring in a very timely fashion and is likely near completion. For corn, the NASS June estimate of planted acreage is 3.5 percent larger than acreage reported to FSA so far this year. For soybeans the NASS acreage estimate is 2.1 percent larger than acreage reported to FSA. The relationship between current NASS and FSA planted acreage estimates are already within the range of the final relationship in the previous nine years.”

What is to be concluded from this historical perspective? 

“First, available evidence suggests that the NASS final estimate of planted, and therefore harvested, acreage will not differ appreciably from the current estimates for either corn or soybeans,” Good says. “Second, the more recent, 20 years, historical pattern of changes in yield forecasts from September to January suggests slightly higher odds for January corn and soybean yield estimates to exceed the September forecasts than to be below the September forecasts. The longer history, 40 years also suggests higher odds of a soybean yield increase, but reflects more of a toss-up for corn yield changes. It seems unlikely, however, that production estimates for either crop will change enough to materially alter the projected supply and consumption balance for the 2016-17 marketing year.”

 

 

Illinois, China study nutritional value of wheat bran for pigs

Published September 16, 2016
  • There is a need to determine the energy contribution from ingredients that are rich in fiber, because these ingredients are increasingly being fed to save on feed costs.
  • Inclusion of 0, 15, or 30 percent wheat bran in diets fed to growing pigs resulted in a decrease in dietary digestible energy, metabolizable energy, and net energy.
  • Values for digestible, metabolizable, and net energy in wheat bran determined using the difference procedure were in good agreement with the values estimated using linear regression, indicating that both procedures may be used to estimate energy values in feed ingredients.

URBANA, Ill. - Research conducted by the University of Illinois is helping determine the nutritional value of wheat bran in diets fed to pigs. Wheat bran, like many other co-products from the human food industries, contains more fiber than corn and soybean meal, which adversely affects energy digestibility.

"To save on feed costs, more producers are turning to co-products,” says Hans H. Stein, professor of animal sciences at Illinois. "Therefore, there is a need to determine the energy contribution from fiber-rich ingredients. But the effect of dietary fiber on heat production and net energy of diets is unclear."

In collaboration with colleagues at China Agricultural University (CAU) in Beijing, China, the research was conducted in the calorimetry unit at CAU. Growing barrows were fed diets containing 0, 15, or 30 percent wheat bran. The pigs were housed in metabolism crates inside calorimetry chambers built to measure gas exchange and heat production.

The digestible energy (DE), metabolizable energy (ME), and net energy (NE) in the diets declined as more wheat bran was included. The DE content of diets containing no wheat bran was 3,454 kcal/kg, compared with 3,161 kcal/kg in diets containing 30 percent wheat bran. The ME content of the diets decreased from 3,400 to 3,091 kcal/kg, and NE content decreased from 1,808 to 1,458 kcal/kg.

The research also validated a procedure commonly used to determine NE. Using the difference procedure, Stein's team determined the DE, ME, and NE of wheat bran to be 2,168, 2,117, and 896 kcal/kg, respectively. These values were similar to those derived using a regression procedure.

Stein says that DE and ME are usually determined using the difference procedure, but NE is usually determined using regression equations. As far as he knows, nobody has compared values derived from the difference procedure with values derived via regression.

"Because experiments to determine NE via the difference procedure are more difficult to conduct than determining DE and ME, it's helpful to know that using regression to determine NE will yield an accurate value," Stein concludes.

The paper, "Wheat bran reduces concentrations of digestible, metabolizable, and net energy in diets fed to pigs, but energy values in wheat bran determined by the difference procedure are not different from values estimated from a linear regression procedure," is published in the July 2016 issue of the Journal of Animal Science. It was co-authored by Neil Jaworski of the University of Illinois, and Dewen Liu and Defa Li of China Agricultural University in Beijing. The full text is available online at https://www.animalsciencepublications.org/publications/jas/articles/94/7/3012.

 

Nov18

NRES Departmental Seminar by Dr. Pierre Gentine

3:00 PM - 4:00 PM
W-109 Turner Hall, 1102 S. Goodwin Avenue, Urbana, IL

Seminar by Dr. Pierre Gentine, Columbia University

Title: Vegetation and droughts in models and observations

Speaker's Website: http://www.columbia.edu/~pg2328/Website/Pierre_Gentines_Homepage/Home.html

For more information, or to meet with this speaker, please contact host Dr. Kaiyu Guan at kaiyug@illinois.edu.

Sustainable Student Farm open house and field tours

Published September 13, 2016

URBANA, Ill. – The University of Illinois Sustainable Student Farm (SSF) and Woody Perennial Polyculture (WPP) project will host an open house on Friday, Sept.16, from 3 to 6 p.m. at their site just south of the main Urbana campus.

The SSF serves as a production farm to provide U of I residence halls with locally grown, low-input sustainable food. In addition, the farm acts as a living laboratory to connect students, community members, and the state at large with regional, small-scale food systems.

The WPP project, located near the SSF, is the first large-scale, university-funded research site studying a savanna-based agroecosystem. Founded in 2012, the WPP site hopes to lay the foundation for a scientific understanding of the potential agricultural and ecological benefits of woody polyculture systems.

During the open house, U of I Dining Services will be serving delicious and free food and drink prepared from SSF produce. The SSF, the WPP, and the U of I Community Garden Plots will be giving tours throughout the afternoon.

Also included in the open house:

  • The Fresh Press will be on hand for information about its new fiber garden and possible demonstrations.
  • The U of I Architecture Department will be talking about farm stand display pieces and a washing/packing/shed complex members of the department built for the SSF.
  • The Student Sustainability Committee, along with other affiliated groups will be on hand with information about projects happening on campus.
  • College of ACES researchers will give presentations on current projects at the SSF and WPP.

Currently the SSF operates between 45 to 48 weeks per year, occupying 6 acres for outdoor field production and nearly 10,000 square feet of year-round high tunnel production. In addition to selling the majority of its produce to the residence halls, it also markets its produce directly to consumers on the U of I quad each Thursday from May to November.

The Sustainable Student Farm was created through a grant from the Student Sustainability Committee and is made possible by the continued support of the University of Illinois Dining Services, the Department of Crop Sciences, and the Student Sustainability Committee.

The farms are located at Lincoln Avenue and Windsor Road, just south of the main U of I campus in Urbana.

For more information about the Sustainable Student Farm, visit http://thefarm.illinois.edu/. Find out more about the WPP research project at wppresearch.org.

News Source:

Matt Turino

Large US corn and soybean production prospects confirmed

Published September 12, 2016

URBANA, Ill. – The USDA just released the September Crop Production and World Agricultural Supply and Demand Estimates (WASDE) reports.  According to a University of Illinois agricultural economist, market participants anticipated the new forecasts of the size of the 2016 U.S. corn and soybean crops and the implications for the level of stocks at the end of the marketing year that started on Sept. 1. However, given the current environment of low crop prices, particularly for corn, all changes from the August forecasts of world production and consumption will be viewed with interest.

Last month, the USDA forecast the U.S. average corn yield at 175.1 bushels per acre, resulting in a production forecast of a record-large crop of 15.153 billion bushels. The September forecast is for an average yield of 174.4 bushels and a crop of 15.093 billion bushels. The corn yield forecast was reduced by five bushels for South Dakota and Tennessee, but increased by six bushels for Kansas and five bushels for Michigan.

The estimated size of the 2016 Brazilian corn crop was reduced by 60 million bushels and the crop is estimated to be 710 million bushels smaller than the 2015 harvest. The 2017 Brazilian crop is projected at 3.25 billion bushels, 610 million bushels larger than the 2016 crop and 100 million bushels smaller than the 2015 crop. Argentine corn production is expected to grow by 335 million bushels (30 percent). Corn production outside of the U.S. is projected at 25.323 billion bushels, slightly smaller than the August forecast, but 1.17 billion larger than the previous crop.   

“Consistent with our analysis of last week, the estimate of 2015-16 marketing-year exports of U.S. corn was reduced by 10 million bushels, to a total of 1.915 billion bushels,” says Darrel Good. “Year-ending stocks, to be estimated in the USDA’s Sept. 30 Grain Stocks report, are projected at 1.716 billion bushels, 10 million larger than last month’s forecast. For the 2016-17 marketing year, the forecast of feed and residual use was lowered by 25 million bushels to reflect the smaller crop forecast. Projected feed and residual use of 5.65 billion bushels is still 450 million bushels (8.7 percent) larger than the forecast for the year just ended. The estimate of feed and residual use for the 2015-16 marketing year will be finalized with the estimate of Sept. 1 stocks to be released on Sept. 30,” he said.

Good says U.S. corn exports are expected to grow to 2.175 billion bushels during the current marketing year as the small 2016 Brazilian crop keeps U.S. corn very competitive in the world market for several more months. Stocks at the end of the current marketing year that began on Sept. 1 are projected at 2.384 billion bushels, just 25 million bushels less than projected last month. Stocks at the projected level represent 16.5 percent of projected marketing-year consumption, the largest ratio in 11 years, but still modest by historic standards. Year-ending stocks last exceeded two billion bushels in 2005 and those stocks represented 19.8 percent of marketing-year consumption. The USDA projects the 2016-17 marketing-year average farm price in a range of $2.90 to $3.50, 5 cents higher than last month’s projection. The average price for the 2015-16 marketing year is projected at $3.60 per bushel.

Last month, the USDA forecast the U.S. average soybean yield at 48.9 bushels per acre, resulting in a production forecast of a record-large crop of 4.06 billion bushels. The September forecast is for an average yield of 50.6 bushels and a crop of 4.201 billion bushels. The soybean yield forecast was increased by three bushels for Indiana, Kentucky, and Tennessee and by four bushels for Illinois and Kansas. The Illinois average yield is projected at 61 bushels per acre. The 2017 Brazilian soybean crop is projected at 3.711 billion bushels, 165 million larger than the 2016 crop, but about 75 million less than projected last month.

“Consistent with our analysis of last week, the estimate of 2015-16 marketing-year exports of U.S. soybeans was increased by 60 million bushels, to a total of 1.94 billion bushels,” Good says. “Year-ending stocks, to be estimated in the USDA’s Sept. 30 Grain Stocks report, are projected at 195 million bushels, 60 million smaller than last month’s forecast. For the 2016-17 marketing year, the forecast of the domestic crush was increased by 10 million bushels, to a total of 1.95 billion, and the projection of exports was increased by 35 million bushels, to a total of 1.985 billion.

Stocks at the end of the current marketing year that began on Sept. 1 are projected at 365 million bushels, 35 million bushels larger than projected last month.  At the projected level, stocks would represent 9 percent of projected use, just marginally higher than the ratio for the 2015-16 marketing year. The USDA projects the 2016-17 marketing-year average farm price in a range of $8.30 to $9.80, 5 cents lower than last month’s projection. The average price for the 2015-16 marketing year is projected at $8.95 per bushel.

“The U.S. corn and soybean crops have been very large in each of the past four years, including the current year,” Good says. “Due in part to the shortfall in South American production in 2016, the consecutive large crops is expected to result in relatively modest inventories of U.S. corn and soybeans at the end of the current marketing year. While the build-up in stocks has pushed prices to below break-even levels for many producers, particularly for corn, prices have remained well above the levels experienced prior to 2006-07.  With a return to more normal levels of production in South America in 2017, however, a supply reduction somewhere else in the world may be required to bring prices back to levels experienced prior to the decline that began in 2014-15.”

 

 

 

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