Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights A1

South Atlantic Area 

Fiscal Year 2009-2011 

Research Highlights

United States Department of Agriculture

Agricultural Research Service

United States

Department

of Agriculture

Agricultural

Research

Service
A2 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Foreword

In the following pages you will find articles about the work of the Agricultural Research 

Service (ARS) in its South Atlantic Area. You may not be familiar with us, so let us take 

this opportunity to introduce you to ARS, the principal in-house research agency of the 

U.S. Department of Agriculture (USDA). 

Congress first authorized federally supported agricultural research in the Organic Act 

of 1862, establishing what is now USDA. That statute directed the Commissioner of 

Agriculture “to acquire and preserve in his Department all information he can obtain by 

means of books and correspondence, and by practical and scientific experiments.” 

The scope of USDA’s agricultural research programs extends far beyond Congress’s 

vision of 1862. Today, agricultural research has a direct impact on nearly all aspects of 

modern life. Our scientists not only study crops and livestock to improve quality and 

quantity but they also devise new ways of using those crops to add value to our lives, 

increase exports, improve human health, and protect the environment. 

We in ARS, like all Americans, are very concerned about safe and nutritious food. 

We study the bugs that cause foodborne illness and find ways to reduce or eliminate 

unwanted pests from the food supply. If agricultural problems arise, such as a new 

disease of crops or livestock, we have the capacity to respond rapidly to find safe and 

appropriate solutions. 

We care deeply about the environment. Extensive programs in the ARS South Atlantic 

Area focus on preserving and improving soil, air, and water quality. We are finding 

new and innovative ways to manage animal wastes, prevent soil erosion, and eliminate 

pesticides from surface water and groundwater. 

These examples represent only a few of the ARS research programs dedicated to 

maintaining and enhancing the economic strength of U.S. agriculture, while improving the 

quality of life for every American. In this volume you will find some facts about the South 

Atlantic Area, a list of the research units, where they are located, and the people you can 

contact for further information. We are delighted that you are reviewing this volume and 

hope that you will find the articles useful and interesting. Please let us know if we can be 

of service to you. 

Deborah L. Brennan, Area Director 

S. Karl Narang, Associate Area Director
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 1

The articles in this volume are reprinted 

from Agricultural Research magazine, 

which is published by the U.S. 

Department of Agriculture, Agricultural 

Research Service, 5601 Sunnyside 

Ave., Beltsville, MD 20705-5129; 

phone (301) 504-1651. The magazine is 

available on the World Wide Web at ars.

usda.gov/ar. 

To subscribe to Agricultural Research

by mail, please contact New Orders, 

Superintendent of Documents, P.O. Box 

371954, Pittsburgh, PA 15250-7954.

This reprint volume may report research 

involving pesticides. It does not contain 

recommendations for their use, nor does 

it imply that uses discussed herein have 

been registered. All uses of pesticides 

must be registered by appropriate state 

and/or federal agencies before they can 

be recommended.

Reference to any commercial product or 

service is made with the understanding 

that no discrimination is intended and 

no endorsement by USDA is implied.

The U.S. Department of Agriculture 

(USDA) prohibits discrimination in 

all its programs and activities on the 

basis of race, color, national origin, age, 

disability, and where applicable, sex, 

marital status, familial status, parental 

status, religion, sexual orientation, 

genetic information, political beliefs, 

reprisal, or because all or part of an 

individual’s income is derived from 

any public assistance program. (Not all 

prohibited bases apply to all programs.) 

Persons with disabilities who require 

alternative means for communication 

of program information (Braille, large 

print, audiotape, etc.) should contact 

USDA’s TARGET Center at (202) 

720-2600 (voice and TDD). To file 

a complaint of discrimination, write 

to USDA, Director, Office of Civil 

Rights, 1400 Independence Avenue, 

S.W., Washington, D.C. 20250-9410, 

or call (800) 795-3272 (voice) or (202) 

720-6382 (TDD). USDA is an equal 

opportunity provider and employer.

Issued October 2012

Contents

 3 Nasonia Wasp Genome Completed

 4 A Better Way To Spot Eggshell Cracks

 6 Growing Premium Seafood—Inland!

 9 Luring Varroa Mites to Their Doom

10 Controlling Fire Ants Takes a Group Effort

12 Collectively Facing an Ugly Rust

14 Tracking Salmonella’s Evolution From Innocuous to Virulent 

16 Tiny Moth Tackles Old World Climbing Fern

18 Flu Fighters: Identifying, Treating, and Preventing the Flu With Help 

From ARS Research

20 Closing In on a Citrus Killer

22 Soybean & Wheat Response to Climate Change

24 Why Watermelons Just Grow and Grow

26 Using Floating Vegetated Mats To Treat Fishery Wastewater

27 New Device Eavesdrops on Insect Pests

28 Producers and Pigs Profit From Manure Management Process

31 Unraveling the Origins of a Symbol of the Tropics 

32 Preparing Peanuts for the Future: New Cultivars and Farming 

 Strategies

34 Opening up a New World of Maize Traits

37 Want To Know What a Gene Does? Use a Little MAGIC

38 Protecting Corn Crops From Aflatoxin

41 Identifying Trees Infected With Citrus Greening

42 “Fire Gel” Protects Beneficial Nematodes From Sun

45 Pickle Spoilage Culprit: May Give the Environment a Helping Hand

46 Citrus Chemical Call to Arms Found

48 Investigating Two Pathways to Replacing Methyl Bromide

50 Egg Quality Preserved After Exposure to Egg Crack Detection 

Technology

50 New Primer Helps Identify More DNA Markers

51 A New Approach to an Old Problem: Devising Formulas To Enhance 

Growth

52 Boosting Barley for Bioenergy

53 Wheat: ARS Wheat Rust Resistance Roundup

54 Throwing a Citrus Pest Off Its Scent
2 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

55 Newcastle Disease Virus Vaccine on the Horizon

56 Archiving Parasites and Protozoa for Research, Diagnoses, and More

57 Troublesome Microbes That Resist Antimicrobials: The 

Antimicrobial Resistance Collection

57 Ozone Erodes CO2 Benefits for Plants

58 Breeding Plants for a High-Ozone World

59 Ozone: Plants Don’t Like It

61 Helping Growers Adapt to Changing Rules on Fumigants

63 Cattle Pastures May Improve Soil Quality

64 New Red Imported Fire Ant Enemies in Place for Fight

65 Science Updates

69 South Atlantic Area Award Winners

76 South Atlantic Area Contacts, Research Units, and Their Locations 

Cover: The broad scope of scientific efforts in the South Atlantic Area 

includes research on parasitic wasps, composting, wheat, weevils, peaches, 

caterpillars, pigs, citrus greening, soybean roots, Iris plants, and peanuts.
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 3

T

used this data and that of the Institute 

for Genomic Research to complete the 

Nasonia genome, which is expected to be 

released this year (2009).

“Nasonia are excellent organisms for 

research and teaching,” says Hunter. 

“They’ve been the subject of genetic, ecological, evolutionary, and developmental 

research for more than 40 years.”

Parasitic wasps, such as Nasonia, are 

extremely important regulators of agricultural pests. Biological control programs 

using parasitoid wasps save about $20 

billion annually by preventing crop losses 

to invasive species in the United States. 

These wasps have been a major benefit to 

food production for humans by reducing 

the amount of food crops destroyed by 

pests and reducing the need for pesticides.

For all these reasons, Nasonia was the 

logical first choice for sequencing of a 

parasitoid genome. Information from 

the genome is being used to identify 

important genes in parasitoid biology, 

and there is broad interest in using the 

Nasonia genome to identify and annotate 

genes involved in important biological 

processes—such as sense of smell, behavior, and even enzymatic pathways.

More information on the Nasonia Genome Project and the genome sequencing can be found at www.rochester.edu/

College/BIO/labs/WerrenLab/nasonia/

genomeprojectindex.html.—By Alfredo 

Flores, ARS.

This research is part of Crop Protection 

and Quarantine, an ARS national program 

(#304) described on the World Wide Web 

at www.nps.ars.usda.gov.

Wayne B. Hunter is in the USDA-ARS 

U.S. Horticultural Research Laboratory, 

2001 South Rock Rd., Fort Pierce, FL 

34945; phone (772) 462-5898, fax (772) 

462-5986, e-mail wayne.hunter@ars.

usda.gov. X

Nasonia

Parasitic wasp, Nasonia vitripennis. 

JACK WERREN (D1479-1)

he genome of Nasonia, a parasitoid 

wasp used for genetic research 

since the 1950s, has been completed. This is big news in the 

genetics research community both domestically and around the globe, since the 

wasp is emerging as a new model system 

in genetics. 

Scientists at the U.S. Horticultural 

Research Laboratory (USHRL) in Fort 

Pierce, Florida, played key roles in the 

efforts to unravel the genome.

The Nasonia genus consists of three 

closely related wasps: N. vitripennis, N. 

giraulti, and N. longicornis. These small 

insects seek out flies—notably blow flies, 

flesh flies, and house flies—then sting and 

lay their eggs in the fly pupae.

Nasonia are easy to work with in the 

laboratory, produce large families, and 

have a short generation time, which is the 

average age at which a female produces 

offspring. Visible and molecular markers 

are available in Nasonia, as well as additional genetic resources, and hosts for 

the wasps are available commercially and 

are easy to rear.

The project’s genesis was in 2003, when 

ARS held a genetics symposium hosted by 

national program leader Kevin Hackett. 

In that meeting it was identified that 

additional work on parasitoid genomics 

was needed. Through some fact checking, 

USHRL entomologist Wayne Hunter 

found that University of Rochester (New 

York) genetics professor Jack Werren had 

already begun Nasonia genomics work. 

Hunter helped to produce genetic libraries 

and sequence some 10,000 expressed 

sequence tags of the genome. Werren 
4 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

N With this in mind, the ARS researchers developed a new technology that allows tiny cracks to 

be more obvious. It can also spot other blemishes 

on an egg that are assumed to be cracks but really 

aren’t. The technology uses a pressure chamber 

and an imaging system that makes even the tiniest 

fractures more apparent.

Technology Emulates Human Graders

The idea is based on one of the basic methods 

human graders use to identify egg cracks: They 

gently tap two eggs together and listen for a dull 

sound. “This technique relies on the acoustic 

properties of the egg. In other words, a cracked 

egg makes a different sound that an intact one,” 

says Jones.

The second method is simply to visually inspect the egg for a crack. “If there’s a feature that 

looks like it might be a crack or if the grader hears 

the indicative sound of a cracked egg, they’ll 

press and/or squeeze the egg to help confirm the 

presence of a crack,” Jones explains.

Initial research with an imaging system tried 

to emulate the visual inspection. But too many 

noncrack shell features were perceived as cracks, leading to 

A Better

Way To

Spot 

Eggshell 

Cracks

ARS-developed 

procedure makes 

tiny cracks 

(microcracks) in 

this egg visible.

A specialized camera 

captures images of 

illuminated eggs inside this 

see-through case. Inside, 

the eggs are subjected to 

a slight vacuum (negative 

pressure) that enhances 

existing shell microcracks, 

making them more visible.

JERRY HEITSCHMIDT (D1314-1)

STEPHEN AUSMUS (D1309-7)

ARS-developed 

procedure makes 

tiny cracks 

(microcracks) in 

this egg visible.

obody wants to buy a carton of eggs 

only to find that some are cracked. 

So naturally cracks are a key factor in 

processing and grading table eggs. But 

some cracks, called “microcracks,” are 

so small that even an experienced human grader’s 

eye can miss them at the processing plant. Unfortunately, the microcracks grow over time and 

are often easily visible by the time they reach 

consumers at market.

Cracks are a food-safety concern because they 

can allow contamination of the egg by pathogens, 

such as Salmonella. Fortunately, safety procedures for eggs begin long before the consumer 

buys a carton. 

The USDA’s Agricultural Marketing Service 

(AMS), which regulates eggs, needed a more 

objective method to detect microcracks—one that 

is simple and inexpensive and works in a batch 

system. They turned to Agricultural Research 

Service (ARS) scientists for a solution.

The ARS team included food technologist 

Deana Jones, at the Egg Safety and Quality Research Unit, and engineers Kurt Lawrence, Seung 

Chul Yoon, and Bosoon Park, image analyst Jerry Heitschmidt, 

and technician Allan Savage, at the Quality and Safety Assessment Research Unit. They designed and built a device that helps 

find those hard-to-see cracks. Both research units are part of the 

Richard B. Russell Research Center in Athens, Georgia. A patent 

application for the technology has been filed.

The Old Way’s the Hard Way

Currently, many high-speed egg-processing plants use highfrequency analysis to “listen” for cracks, says Lawrence. Other 

plants still do it the old-fashioned way, with human graders 

visually inspecting eggs with a bright light source in a low-light 

environment.

It is impossible to detect all cracks, so a few are always missed; 

but the problem is that no method picks up the microcracks. The 

result is that some cartons—by the time they get to market—may 

have eggs with too many cracks. Another problem is that current 

methods may unnecessarily remove eggs that are thought to be 

cracked but really aren’t—what scientists call a “false positive.”

Advances in modern egg-grading machines have resulted in 

the processing of up to 180,000 table eggs per hour. Processing 

plants that operate under USDA grading certification practices 

are required to have a certain portion of their eggs graded by 

AMS human graders. In the largest plants, the limiting factor for 

processing speed is the grader—so there’s a need for a second 

person to handle the volume.
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 5

numerous false positives. So the researchers needed a method 

to enhance cracks—similar to the way human graders squeeze 

the egg along the crack to see if it opens. “The question for us 

then became how to automatically press along a crack that can 

be located anywhere on an egg shell and in any orientation,” 

says Lawrence.

Further engineering research was in order. It was at that 

point the scientists realized that the wrong question was being 

asked—or rather, the answer didn’t fit the question. The detection system could not press or squeeze the egg like the graders 

did, but what would happen if they could pull on the egg with 

a slight negative pressure, or vacuum? 

It was like a lightning bolt of inspiration—and that’s what 

a crack looks like to the camera when it opens under pressure. 

The first prototype chamber was built for a single egg, but the 

scientist quickly expanded it to a 20-egg chamber.

To test the chamber, 1,000 white-shell table eggs were obtained from a nearby egg-processing facility, transported to 

the laboratory, and brought to room temperature to simulate 

processing conditions. Many of the eggs were manipulated to 

cause microcracks and were immediately examined by AMS 

graders and scored as either intact or cracked. The eggs were then 

subjected to the negative pressure/imaging system and regraded.

The results were surprising. “The system detected 99.4 

percent of the eggshell cracks while recording almost no false 

positives—0.3 percent—for an overall accuracy of 99.6 percent. 

In comparison, the professional human graders had 85.8 percent 

crack detection and 1.2 percent false positives, with an overall 

accuracy of 94.2 percent on these hard-to-see microcracked 

eggs,” Lawrence says. “The system’s results are much better 

than anyone had achieved earlier.

“This could very well provide a tool that egg graders can use 

to consistently identify cracked eggs and improve the quality of 

the eggs that reach the consumer.”—By Sharon Durham, ARS.

This research is part of Food Safety, an ARS national program 

(#108) described on the World Wide Web at www.nps.ars.usda.

gov.

Kurt Lawrence is in the USDA-ARS Quality and Safety 

Assessment Research Unit, Richard B. Russell Research Center, 

950 College Station Rd., Athens, GA 30605; phone (706) 546-

3527, fax (706) 546-3607, e-mail kurt.lawrence@ars.usda.gov.

Deana Jones is in the USDA-ARS Egg Safety and Quality 

Research Unit, Richard B. Russell Research Center, 950 College 

Station Rd., Athens, GA 30605; phone (706) 546-3486, fax (706) 

546-3035, e-mail deana.jones@ars.usda.gov. X

Food technologist 

Deana Jones 

(foreground) and 

hyperspectral imaging 

specialist Jerry 

Heitschmidt examine 

eggs for shell quality 

defects as biological 

science aide Vicky 

Broussard uses a 

pressure device to test 

eggs for cracks.

STEPHEN AUSMUS (D1310-7)
6 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

into and out of tanks every year. What’s more, RAS-based fish 

farms could provide an alternative to today’s practice of raising 

marine fish in net cages or pens in the ocean. RAS production of 

seafood could diminish unwanted spread of nutrients from feed 

or fish wastes, reduce risk of diseases being transmitted from 

domesticated fish to their seagoing brethren or vice versa, and 

avoid unplanned breeding.

But before these low-salinity farms for seafood can become 

a reality, much more remains to be discovered about the needs 

of the saltwater fish that would be reared in them. In addition to 

figuring out the biological realities of raising these fish, there’s 

a myriad of engineering details to be worked out. After all, the 

RAS technology was designed for freshwater—not saltwater—

fish farms. For example, some of today’s RAS filtering technology is about 30 percent less efficient in handling seawater than 

freshwater.

A team of ARS aquaculture researchers in the southeast 

Florida city of Fort Pierce are tackling all these issues. Fish 

Growing Premium Seafood—Inland!

P

Agricultural engineer Timothy Pfeiffer uses a hand-held meter to 

measure water quality in a moving bed biofilter.

Fish nutritionist Marty Riche feeds juvenile Florida pompano during 

studies to determine appropriate feeds and feeding-management 

practices for profitable inland production of saltwater fish. 

STEPHEN AUSMUS (D1341-10) STEPHEN AUSMUS (D1228-11)

eople who know seafood know that cobia and Florida 

pompano are among the world’s best. Found in the warm 

waters off the Atlantic and Gulf coasts, these saltwater 

superstars are prized for both commercial and sport 

fishing. Pompano (pronounced POM-puh-no) and cobia (COEbee-uh) have firm, mostly white flesh that’s perfect for grilling, 

pan-frying, or baking. Some people find that pompano has a 

pleasing, slightly sweet note.

Pompano is flat and silvery, and looks something like sunfish. 

Cobia is long and sleek, with a silver stripe on its dark-grey 

sides. Both of these scrumptious seafarers command premium 

prices—sometimes as much as $30 a pound filleted.

Someday, pompano, cobia, and other marine finfish might 

be commonly raised inland, hundreds of miles from the nearest 

ocean or bay. They’d be reared in huge tanks of water—fresh or 

slightly salty—in what’s known as a “recirculating aquaculture 

system” (RAS).

These systems, in which water is cleaned and used again 

and again, are referred to as “closed” because they’re almost 

completely self-contained. They offer the potential to reduce 

discharge of everyday fish-farm effluent to as little as 3 percent—or less—of the total amount of water used each day. All 

the effluent could be treated to make it suitable to apply on land 

(if it’s freshwater) or to artificial saltwater marshes (if it’s lowsalinity wastewater).

The fish waste and unused food collected in the system’s 

filters could be used as nutrient-rich compost or perhaps for 

generating methane. 

These water-sparing systems present an alternative to coastside 

flow-through operations that run millions of gallons of seawater 
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 7

biologist Chuck Weirich, fish nutritionist Marty Riche, and 

agricultural engineer Tim Pfeiffer are based at the Harbor 

Branch Oceanographic Institute. Part of Florida Atlantic 

University, the institute is one of many organizations 

with which the team collaborates. The ARS research is 

managed through the Arkansas-based Harry K. Dupree Stuttgart National Aquaculture Research Center.

Spawning Success

To make the systems a commercial and environmental 

success requires taking a close look at every aspect of the 

lives of the fish—from spawning by the parents, or broodstock, 

to the needs of the larvae, or seedstock, that emerge from the 

tiny eggs, to the requirements of the fingerlings, the juvenile fish 

that end up as delectable fillets or, in some cases, broodstock.

Every detail—from how to coax broodstock to spawn all year 

round to how much ammonia and nitrate buildup fingerlings 

can tolerate in their recirculating tanks—has to be tested. With 

this new knowledge, growers who invest in the RAS technology should have a better chance of making their new-age fish 

farms profitable.

In an experiment with 2,400 juvenile pompano, the scientists 

showed that it’s indeed possible to raise this species in water 

that’s only slightly salty. In this case, the water had a salinity 

of only 5 parts per thousand as compared to the 35 parts per 

thousand in most of the world’s oceans.

The accomplishment is a remarkable scientific first. It provides 

important proof that the concept of raising saltwater species in 

nearly fresh water—an alien environment to which the animals 

are not adapted—can be done for short periods of time. In this 

case, the pompano that the researchers reared from juveniles to 

healthy, harvest-ready adults lived in the low-salinity water of 

the “grow-out tanks,” as they are called, for only 110 days. What 

remains is to make the system practical, profitable, and energy 

efficient for not just the grow-out phase but for the broodstock 

and hatchery phases, as well.

Food, Water, and Room To Grow

What to feed the saltwater fish during the various stages of their 

captive lives is, of course, one of the most pressing questions. 

In a study with 50,000 pompano larvae, fish biologist Weirich 

and colleagues learned more about the feeding habits of these 

baby fish. For the study, the researchers used digital photography 

and image-analysis software to observe and record the larvae, 

which, in their earliest days, are transparent and look something 

like tadpoles.

The scientists determined the optimum size classes of two 

kinds of live prey—brine shrimp and tiny organisms called 

“rotifers.” At various stages of their growth, the little fish are 

capable of catching and eating these snacks as they swim by. 

During this growth phase, the upper and lower jaws of the larvae, 

and their miniature digestive systems, are still developing. The 

fish are born with their mouths closed, and the size of the opening, 

or “gape,” that develops determines the size of the food—in 

their case, rotifers and brine shrimp—that they’re able to nab 

and swallow.

In new studies, Weirich and colleague Riche are determining 

how to wean the larvae off of these live feeds more quickly. 

That’s because cultivating live feeds for the infant fish is more 

costly and labor-intensive than simply giving them dry feeds. 

Those feeds won’t appear on their menu until the fish have made 

the transition from larvae to juvenile.

Moving juveniles from the nursery tanks to the world of 

the grow-out tanks—where they’ll develop to market-ready 

weights—poses the question of how many of these young fish 

can be put into a tank without overcrowding them.

Overstocking can cause stress and may increase risk of disease, 

reduce growth rates, and create other problems that can bite into 

profits. Weirich, Harbor Branch Oceanographic Institute colleague Paul Wills, and Riche found that pompano stocked at the 

rate of 200 fish per tank weighed about 1.5 pounds at harvest, 

making them about 10 percent heavier than pompano stocked 

at a rate of 400 per tank.

But a cobia study by Weirich and Wills showed no significant 

difference in their survival, or weight at harvest, regardless of 

whether the fish were stocked at a low (35 fish per tank), medium 

(70 fish), or high (106 fish) density. At the end of the study, all 

the cobia weighed about the same. Each yielded two generously 

sized fillets.

No matter what the stocking rate, finfish won’t flourish in 

recirculating tanks if there are life-threatening problems with 

the quality of the water. To keep the recirculating water clean 

and to limit risk of disease, the researchers are determining the 

most cost-effective use of what are known as “biofilters.” These 

devices contain bacteria that convert the toxic ammonia in fish 

waste into less-toxic forms (nitrite and nitrate). In other work, 

they’re evaluating alternative methods to efficiently remove 

solids—such as waste and uneaten feed—from the system.

Fishery biologist Charles Weirich uses image 

analysis to determine optimal sizes of live prey, 

such as this brine shrimp (left), for fish larvae to 

consume. (Magnified about 30x.)

CHARLES WEIRICH (D1346-1)
8 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Pfeiffer is leading studies of what is known as “airlift technology” to power the system’s water-treatment components. Airlift 

systems can cut energy costs because they use less electricity 

than conventional centrifugal pumps for moving water.

There’s an additional twist to the engineering and design 

research: The water-quality requirements of each species may 

differ, and what works to keep one species healthy and fast growing might not succeed with another. That means the components, 

or combinations of components, may have to be customized.

Much remains to be learned about the fish and the recirculating systems. And even when the technology is ready to use, no 

one can predict how long it will then take before inland farming 

of seafood—in these recirculating tanks—becomes as common 

as on-land farming of rainbow trout or catfish. For people living far from the sea, who’d like to be able to buy fresh, locally 

raised seafood at their neighborhood supermarket, environmentally responsible inland mariculture simply can’t happen soon 

enough.—By Marcia Wood, ARS.

This research is part of Aquaculture, an ARS national 

program (#106) described on the World Wide Web at www.

nps.ars.usda.gov.

Charles R. Weirich, Martin A. Riche, and Timothy J. 

Pfeiffer are with the USDA-ARS Harry K. Dupree Stuttgart 

National Aquaculture Research Center, c/o Harbor Branch 

Oceanographic Institute, 5600 Hwy. U.S. 1 N., Fort Pierce, 

FL 34946; phone (772) 465-2400, ext. 471 [Weirich], ext. 

638 [Riche], ext. 360 [Pfeiffer], fax (772) 466-6590, e-mail 

charles.weirich@ars.usda.gov, marty.riche@ars.usda.gov, 

timothy.pfeiffer@ars.usda.gov. X

Marty Riche and technician Patrick Tracy harvest market-size 

Florida pompano from grow-out tanks at the Harbor Branch 

Oceanographic Institute (HBOI) to determine growth rates during 

feed nutrition studies. 

Using tissue and enzyme assays and growth data, Marty Riche 

develops feeds for marine fish grown in low-salinity water. 

Assisted by HBOI technician Terri Breeden (left) and ARS 

technician Todd Lenger (center), ARS fish biologist Charles 

Weirich measures and weighs cobia grown in recirculating 

aquaculture systems.

Right: 

Charles 

Weirich 

(left), HBOI 

biological 

scientist 

Fernando 

Cavalin 

(center), 

and HBOI 

technician 

Meghan 

Anderson 

study a 

sample of 

hundreds 

of pompano 

larvae. 

STEPHEN AUSMUS (D1227-2)

 STEPHEN AUSMUS (D1230-5)

 STEPHEN AUSMUS (D1226-34)

STEPHEN AUSMUS (D1229-5)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 9

The Varroa mite, Varroa destructor, is only 

about one-sixteenth of an inch long. But 

that hasn’t stopped the eight-legged, bloodsucking parasite from becoming the single 

worst pest of honey bees since first being 

detected in Florida in the 1980s.

Any threat to honey bees is a threat to 

American agriculture. Without them, the 

yield and quality of many flowering crops 

would suffer—almonds, apples, blueberries, cantaloupe, cranberries, and zucchini, 

to name just a few. Indeed, as the chief 

pollinator of these crops, the honey bee’s 

contributions are considered a $14 billion 

asset to our economy—and that’s not even 

counting the honey and beeswax the insect 

produces.

So it is with quite a bit of urgency 

that researchers nationwide are seeking 

new ways to control Varroa, particularly 

methods that will diminish reliance on the 

chemical controls—fluvalinate and coumaphos—now used. At 

the ARS Chemistry Research Unit in Gainesville, Florida, research leader Peter E.A. Teal is testing a bait-and-kill approach 

using sticky boards dosed with natural chemical attractants, 

called “semiochemicals.”

For patenting reasons, Teal won’t reveal what the specific 

compounds are, other than to say they’re naturally produced by 

honey bees and highly attractive to Varroa mites.

In nature, Varroa mites rely on the semiochemicals to locate—

and then feed on the bloodlike hemolymph of—both adult bees 

and their brood, weakening or killing them. Severe infestations 

can decimate an affected hive within several months—and rob 

the beekeeper of profits from honey or pollinating services. But 

in this case, the mites encounter a more heady bouquet of honey 

bee odors that lure them away from their intended hosts and onto 

the sticky boards, where they starve.

Preliminary tests of the attractant have been promising. “For 

example, we are able to induce 35 to 50 percent of mites to 

drop off of bees when we present them with either of the two 

attractants, and more than 60 percent of free mites are attracted 

to these chemicals in biological tests,” Teal reports. Moreover, 

it doesn’t appear that the extra dose of semiochemicals wafting 

through the hive interferes with the honey bees’ normal behavior 

or activity to any significant degree, adds Teal, who, along with 

postdoctoral associate Adrian Duehl and University of Florida 

collaborator Mark J. Carroll, reported the results this past January 

at the 2009 North American Beekeeping Conference in Reno, 

Nevada.

The researchers hope ARS’s patenting of the Varroa attractants 

will encourage an industrial partner to develop the technology 

further for use by beekeepers as both a monitoring tool and an 

alternative to chemical controls.—By Jan Suszkiw, ARS.

This research is part of Crop Protection and Quarantine, an 

ARS national program (#304) described on the World Wide Web 

at www.nps.ars.usda.gov.

Peter E.A. Teal is in the USDA-ARS Chemistry Research Unit, 

Center for Medical, Agricultural, and Veterinary Entomology, 

1600-1700 S.W. 23rd Dr., Gainesville, FL 32608; phone (352) 

374-5730, fax (352) 374-5707, e-mail peter.teal@ars.usda.

gov. X

Luring 

Varroa

Mites 

to Their 

Doom

Varroa mites in a cell of a honey 

bee comb that has been treated 

with attractants identified 

by chemist Peter Teal and 

collaborators. The other cells 

(with no mites) are control cells 

(no attractants). 

ADRIAN DUEHL (D1506-1)
10 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

R

Controlling Fire Ants 

Takes a Group Effort

In studies to determine whether fire ants dominate other 

ants in South America, worker ants of Crematogaster and 

Pheidole, two competitors of the red imported fire ant, 

try to dominate a tuna bait. 

Spores of the microsporidian pathogen 

Kneallhazia solenopsae, a potential 

biocontrol of fire ants. 

SONIA CABRERA (D1492-1)

DAVID OI (D1491-1) 

ed imported fire ants (RIFA), native to South America, accidentally landed in the United States in Mobile, Alabama, 

during the 1930s and advanced across the southern region. 

For more than 20 years, two ARS labs—one in Argentina 

and the other in Florida—have been collaborating in studies 

of RIFA biology and biocontrol in hopes of controlling the pest’s 

numbers in the United States. 

The hunt for biological control of imported fire ants began in the 

1970s in Brazil. The program at ARS’s South American Biological 

Control Laboratory (SABCL) in Hurlingham, Argentina, started 

in 1987. Staff there have since conducted well over 340 field trips 

in Argentina, Bolivia, Brazil, Chile, Paraguay, and Uruguay for 

exploration and monitoring of fire ants and their natural enemies. 

During this time, 350,000 kilometers were covered, 15,000 fire 

ant colonies were collected or examined in the field, and some 150 

fire ant colonies were hand carried to ARS’s Center for Medical, 

Agricultural, and Veterinary Entomology’s (CMAVE) quarantine 

facility in Gainesville, Florida. 

Fire Ants Dominate Other Ants in South America

Scientists at SABCL have studied interactions between RIFA

(Solenopsis invicta) and other aboveground foraging ants in two 

habitats in northeastern Argentina. A combination of pitfall traps 

and baits were used to study day-to-day activity in ant communities to see how the ants interact with one another. Each pitfall trap 

consisted of a 50-milliliter plastic tube buried in the ground and 

half-filled with soapy water, giving the scientists a measure of 

the diversity and abundance of the ant species at the site. The 

bait consisted of 1 gram of commercial canned tuna placed on a 

5-centimeter-diameter plastic card near the trap. Observations 

of ants competing for the bait revealed the dominance abilities 

of each ant species at that site.

Some 28 ant species coexisted with S. invicta in an open 

area of forest along a watercourse, whereas only 10 species 

coexisted with S. invicta in dry forest grassland.

“We found the highest numbers of fire ants in the area near the 

water,” says Luis Calcaterra, a biologist at SABCL who works 

closely with the lab’s director Juan Briano. “But we were surprised 

to see it perform better as a discoverer and a dominator in the dry 

habitat, despite the lack of resources there.”

A more recent, larger scale study of more than 100 ant species in 

natural and modified environments in northern Argentina revealed 

that RIFA is the most numerically dominant species in other habitat 

types as well, says Calcaterra.

Before these studies, it was thought that the fire ant was not 

dominant in its native land. But it proved to be the most numerically and behaviorally dominant, winning 78 percent of interactions 

with other ants, mainly against its most fierce competitor, Pheidole 

obscurithorax, an ant of northern Argentina and Paraguay. In a 

battle with the Argentine ant, Linepithema humile, the fire ant won 

80 percent of the time.

“A quick mass recruitment was the main reason the fire ants were 

able to dominate the baits,” says Calcaterra. “They organize well.”

Though the fire ants were ecologically dominant, the study 

revealed that other species were able to coexist. “It was possible 

because of the relatively poor ability of S. invicta to discover the 
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 11

food resources, but it is also due to the higher ant diversity and 

competitive pressure in its native range compared to its area of 

introduction,” explains Calcaterra. The presence of phorid flies affected the foraging rates of fire ants but had little effect on fire ant 

interactions with other ants.

Biological Control of Red Imported Fire Ants

The technology transfer between CMAVE and SABCL has been 

mutually beneficial. Overall, 36 shipments were made to CMAVE 

from SABCL, and they included 397 fire ant colonies (204 infected 

with diseases, 136 parasitized with phorid flies or parasitic ants, and 

57 healthy). The lab continues to look at the biocontrol potential 

of key candidates—the microsporidia Kneallhazia solenopsae and 

Vairimorpha invictae, phorid flies in the genus Pseudacteon, the 

parasitic ant Solenopsis daguerrei, wasps in the genus Orasema,

and the nematode Allomermis solenopsii.

 “Pathogens like K. solenopsae and V. invictae—alone or in combination—are associated with localized declines of 53-100 percent 

in fire ant populations in Argentina,” says CMAVE entomologist 

David Oi.

And phorid flies, which parasitize and kill fire ants, are now in 

use in the United States to reduce RIFA foraging and help control 

some populations. 

Now, CMAVE and SABCL scientists are looking to add a new 

scientific wrinkle—using the phorid fly as a vector for infecting the 

fire ant population with the microsporidia.

Though preliminary data showed that V. invictae could not be successfully transmitted to phorid flies effectively, K. solenopsae could 

be. Oi, CMAVE entomologists Sanford Porter and Steven Valles, 

and SABCL’s Briano and Calcaterra were able to infect phorid 

flies with K. solenopsae without harming the flies. The next step 

is to determine whether infected flies are able to infect RIFA with 

the microsporidia—providing another mechanism for transmission 

between RIFA colonies. 

“K. solenopsae not only reduces fire ant colony size, it also 

reduces the amount of sexual brood—or reproducing ants, affects 

queen survival, and increases the death rate of colonies,” says Oi.

Other cooperative research between CMAVE and SABCL on 

biological control of fire ants evaluates ecological interactions of 

fire ants and phorid flies in different habitats in Argentina. Genetic 

studies also are being performed at CMAVE with material collected 

in South America to characterize the population structure of the 

parasitic ant S. daguerrei and to determine the source population of 

the fire ants present in the United States and other countries.

 “Our work continues in order to develop novel technologies and 

strategies to control red fire ant populations and mitigate their damage,” says Oi.—By Sharon Durham and Alfredo Flores, ARS.

This research is part of Crop Protection and Quarantine (#304) 

and Veterinary, Medical, and Urban Entomology (#104), two ARS 

national programs described on the World Wide Web at www.nps.

ars.usda.gov.

To reach scientists mentioned in this story, contact Sharon Durham, 

USDA-ARS Information Staff, 5601 Sunnyside Ave., Beltsville, MD 

20705-5129; phone (301) 504-1611, fax (301) 504-1486, e-mail 

sharon.durham@ars.usda.gov. X

A parasitic phorid fly attempts to lay an egg into a 

fire ant worker. If the fly injects microsporidianinfected eggs into the ant, or the ant kills and eats 

the fly, the fire ant will become infected and die. 

A newly hatched 

phorid fly 

emerges from 

the head of a 

red imported 

fire ant that has 

been parasitized 

and killed. 

SANFORD PORTER (D1505-1)

SANFORD PORTER (D1505-2)
12 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Collectively Facing an Ugly Rust

W hen the threat to a food staple like wheat is worldwide, the best way to counter it is to enlist the 

world’s experts in a research coalition. That’s just 

what has been done to answer the very real threat 

of Ug99, a new stem rust to which most of the 

wheat and barley grown in the United States and the rest of the 

world has no resistance.

As part of that global response, the Agricultural Research 

Service became a founding partner in the Borlaug Global Rust 

Initiative (BGRI), in alliance with the International Maize and 

Wheat Improvement Center (CIMMYT), the International Center 

for Agricultural Research in the Dry Areas (ICARDA), the Food 

Close-up of stem rust 

on wheat. 

and Agriculture Organization of the 

United Nations, and Cornell University. 

The BGRI is chaired by Nobel Peace 

Prize winner Norman E. Borlaug.

“To reduce the vulnerability of U.S. 

and global wheat crops to Ug99 requires 

an international partnership of scientists 

and institutions with diverse expertise 

and facilities. We are fortunate that 

ARS was one of the first institutions to 

respond to the call from Dr. Borlaug,” 

says Ravi Singh, BGRI’s chief wheat scientist.

“ARS has several of the world’s small pool of experts in cereal 

rust research,” explains Kay Simmons, ARS national program 

leader for plant genetics and grain crops. “We have several collaborative research projects under way that are feeding critical 

information into BGRI, and these partnerships are the best way 

to leverage everybody’s resources to combat Ug99.”

ARS is partnering with CIMMYT and the Kenya Agricultural 

Research Institute (KARI), to screen wheat and barley lines from 

breeders from all over the United States for Ug99 resistance.

Kenya has had Ug99 since 2001, so having use of the nursery 

there provides a way for U.S. breeders to find out which of their 

new varieties and lines may be able to stand up to the rust without 

JACK DYKINGA (K7878-1)

ARS scientists are 

evaluating U.S. wheat 

lines for rust resistance in 

hopes of giving U.S. wheat 

and barley breeders 

a head start towards 

protecting new varieties 

from Ug99, a deadly 

wheat stem rust in eastern 

Africa.

YUE JIN (K11192-1)

In 1999, a new strain of cereal stem rust was first reported in Uganda, 

hence the name “Ug99.” It was found in Kenya in 2001 and in Ethiopia 

in 2003. Now it has spread to Yemen, Sudan, and Iran.

Stem rust is favored by hot days and mild nights with adequate moisture for nighttime dews, and it is spread by the wind—conditions that 

can occur anywhere wheat grows. Historically, stem rust has been the 

most destructive disease of wheat and barley. ARS has found that nearly 

all spring wheat varieties grown in the United States are susceptible to 

Ug99, as are more than 75 percent of U.S. winter wheat and most of the 

commercial barley varieties.
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 13

bringing the pathogen into the United States and without each 

wheat- or barley-breeding project trying to start its own nursery 

overseas.

More than 5,000 U.S. lines have been evaluated through this 

program so far.

“Everybody wins. Not only does the United States benefit from 

this nursery, but ARS is also sharing all the information from 

these screenings with the other members of BGRI, and they are 

sharing their results with us,” Simmons says.

In fact, researchers from other BRGI members—such as Agriculture and Agri-Food Canada, KARI, and CIMMYT—help 

score the wheats at various points in the growing season alongside ARS scientists such as plant pathologist/geneticist David 

Marshall, research leader of the ARS Plant Science Research 

Unit in Raleigh, North Carolina.

“Results from the 2005-2007 screenings showed that Ug99 

has overcome even more major resistance genes than previously 

believed,” Marshall says. “This only emphasizes how important 

it is to find new ways for wheat to deal with Ug99.”

ARS has also used the test nursery to screen a significant portion of the small-grains germplasm collection in search of new 

sources of resistance.

The information from this screening has helped jump-start a 

cooperative stem rust-resistance breeding program at Oklahoma 

State University. ARS geneticist Michael Pumphrey at the Plant 

Science and Entomology Research Unit, Manhattan, Kansas, 

transferred new resistance genes into germplasm that 

university professor Brett Carver is now incorporating 

into locally adapted breeding populations.

“What ARS accomplished in 2 years would have taken 

us about 5 years, assuming we would have enjoyed the 

same success in crossing with some of the more cantankerous wild wheat relatives used in this project,” Carver 

says. “This partnership allows me to remain focused on 

the locally specific breeding objectives that already have 

my attention.”

Opening a New Window

Recently, the Bill & Melinda Gates Foundation provided a $26.8 million grant to Cornell University to create 

the Durable Rust Resistance in Wheat (DRRW) project, 

which will help bolster Ug99 research. With this grant, 

Cornell University has brought together 15 partnering 

institutions from all over the world, including ARS, with 

the goal of systematically reducing wheat’s vulnerability 

to rust diseases through an international collaboration 

of unprecedented scale and scope, according to Ronnie 

Coffman, DRRW’s principal investigator.

ARS is most heavily involved in three of the project’s 

objectives: tracking wheat rust pathogens, exploring 

whether rice offers any immunity to rust that might be 

transferred to wheat, and discovering new sources of rust resistance in wild wheat and wild barley.

Because most of current Ug99-effective genes are derived 

from relatives of common and durum wheat, ARS is looking to 

wild relatives as a source of genes for new types of resistance. 

Preliminary studies led by plant pathologist Yue Jin at the ARS 

Cereal Disease Laboratory have found some resistance to Ug99 

in einkorn, goatgrass, and sanduri wheat.

ARS will be joining with ICARDA and the University of 

Minnesota to screen other wild relatives of wheat and barley.

“Wheat stem rust is borne by the wind across every political 

boundary where wheat is grown. To monitor it and defeat it, 

international partnerships have always been essential,” Coffman 

says. “Since the beginning of rust research, ARS scientists have 

been good leaders and good partners, working at the forefront 

of science on behalf of the world community. Without their essential participation, the DRRW project would not be possible.”

More information on DRRW can be found at www.wheatrust.

cornell.edu.—By J. Kim Kaplan.

This research is part of Plant Diseases, an ARS national 

program (#303) described on the World Wide Web at www.nps.

ars.usda.gov.

Kay Simmons is the National Program Leader for Plant Genetics and Grain Crops, Room 4-2210, 5601 Sunnyside Ave., 

Beltsville, MD 20705-5139; phone (301) 504-5560, fax (301) 

504-6191, e-mail kay.simmons@ars.usda.gov. X

Nobel Peace Prize winner Norman Borlaug (second from left) believes Ug99 

is the most serious threat to wheat and barley in 50 years. He is shown here 

consulting with Kenyan and CIMMYT leaders near wheat plots in Kenya. 

KAY SIMMONS (D516-1)
14 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

I

Tracking Salmonella’s Evolution From 

Innocuous to Virulent

To better understand how bacteria evolved the ability to get into 

eggs, Jean Guard-Bouldin and technician Cesar Morales analyze 

how many colony types are present in the organs of chickens 

infected with Salmonella. 

STEPHEN AUSMUS (D1335-16)

It is the only Salmonella pathogen that is found inside the egg, 

is present in healthy hens, and is able to cause illness in humans.

“To reduce current levels of infection, we’re studying how S. 

enteritidis evolves and infects hens on the farm,” says GuardBouldin. “Using mutational changes in the Salmonella genome 

as a sort of ‘breadcrumb trail,’ we’ve tried to determine the first 

time this bacterium became capable of getting inside the egg 

from hen reproductive organs.”

Mapping Mutations

The mutational maps for S. enteritidis were obtained by using a 

database from the Sanger Institute to generate a set of primers that 

“tile” the DNA of the test strains. Tiling keeps fluorescent-labeled 

DNA from producing light as a signal. If a signal is produced, that 

means that a mismatch is present in the test strain. All potential 

mismatches, or polymorphisms, are sequenced multiple times in 

multiple strains to identify the exact location and nature of the 

change. To date, 447 polymorphisms have been detected, and 

about half of these have been confirmed by sequencing.

Down the Genome Path

“S. enteritidis, like a lot of other bacteria, is able to reproduce 

very quickly—in optimal conditions, every 20 minutes,” says 

Guard-Bouldin. “Such a fast pace allows the organism to accumulate polymorphisms. Only healthy competitors go on to 

reproduce, survive, and then thrive in the infection pathway to 

the egg.”

Once her mutational maps were complete, Guard-Bouldin 

could apply a mathematical approach that compares the number 

of polymorphisms seen today between strains that have been 

recently isolated to come up with a rate of evolution. This has 

led to a theory that a large-scale swap of DNA about 36 years 

ago occurred between strains in association with the emergence 

of egg contamination. Evolution beginning hundreds of years 

ago, however, probably laid the footing for today’s problem.

While the hybrid strain that recently emerged had the ability to 

contaminate the internal contents of eggs, it also had a problem: 

It was carrying incompatible viruses within its genome.

As a result, says Guard-Bouldin, “The hybrid strain split very 

quickly into two lineages, each carrying one virus. Except for 

the different viruses, the two strains had identical genomes, and 

both contributed to the beginning of the pandemic. Both of the 

newly split lineages continued to evolve by accumulating small 

changes in their genomes. They eventually began to vary in their 

ability to contaminate eggs, to survive on the farm, and to challenge our ability to understand their association with chickens.”

n forensic science, DNA is often the last word. But an 

ARS scientist has found that even having one full DNA 

sequence may not be the definitive answer in the case of 

Salmonella microbes.

A team of researchers led by veterinary medical officer 

Jean Guard-Bouldin at ARS’s Egg Safety and Quality Research 

Unit in Athens, Georgia, has found S. enteritidis strains to be 

so similar genetically that they appear identical—yet they may 

behave differently inside the hen. 

To distinguish between the apparently identical genomes, researchers must use a technique called “whole-genome mutational 

mapping” to analyze multiple strains. It’s a way of comparing 

the genomes to find small differences in DNA—called “polymorphisms”—among them. 

In food safety and public health, S. enteritidis is problematic. 
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 15

Searching for Small Changes

Paula Cray, research leader of ARS’s Bacterial Epidemiology 

and Antimicrobial Resistance Research Unit, also in Athens, was 

able to detect a few of these changes using a more conventional 

method—pulse field gel electrophoresis (PFGE). This method 

provided a baseline for estimating the frequency at which DNA 

changes were being missed. Whereas mutational mapping found 

447 polymorphisms, 12 of which disrupted genes, PFGE found 

only 2 differences between the Salmonella strains that varied in 

the ability to contaminate eggs. 

“In fact, in a comparison of PFGE patterns, every band difference could account for about 200 polymorphisms going 

undetected,” says Guard-Bouldin. Cray’s research is a good 

example of why food safety agencies are continuously testing 

which methods are best for detecting evolutionary trends in 

bacteria that threaten public health.

The New Horizon

The data from this research is being entered into a publicly 

available database by the National Center for Biotechnology 

Information, part of the National Institutes of Health.

“This information about differences between genomes could 

help streamline the process of finding out how human disease 

organisms evolve to become more virulent,” says Guard-Bouldin. 

“The main focus for us now is to continue sequencing entire 

genomes and searching for more genetic changes that help us 

understand the Salmonella organism.

“Up until recently, genomic techniques for delving this deeply 

into the genetic code of multiple Salmonella strains weren’t 

available or cost effective.

 “If we can understand how Salmonella evolved to become 

pathogenic, perhaps we can apply the same principles to other 

foodborne pathogens and begin to study foodborne illness the 

way influenza is being monitored—with equal emphasis on the 

importance of small, as well as large, genetic changes.”

According to the Centers for Disease Control and Prevention, 

about 40,000 cases of salmonellosis are reported in the United 

States every year. Most result in diarrhea, fever, and abdominal 

cramps lasting 4 to 7 days, but severe cases caused about 70 

deaths in 2000. Adequate cooking eliminates the risk of infection 

from eggs.—By Sharon Durham, ARS.

This research is part of Food Safety, an ARS national program 

(#108) described on the World Wide Web at www.nps.ars.usda.

gov.

Jean Guard-Bouldin is in the USDA-ARS Egg Safety and 

Quality Research Unit, Richard B. Russell Research Center, 950 

College Station Rd., Athens, GA 30605; phone (706) 546-3446, 

fax (706) 546-3035, e-mail jean.guard.bouldin@ars.usda.gov. X

An important intermediate step in the analysis of evolution is to 

determine which methods are effective for detecting differences 

between strains. Using a Bio Rad imager and pulse field gel 

electrophoresis, veterinary medical officer Jean Guard-Bouldin (left) 

and technicians Carolina Hall (center) and Cheryl Pearson-Gresham 

classify strains that are being used to produce mutational maps. 

A typical egg contamination experiment often 

involves as many as 1,000 eggs. Here, Jean 

Guard-Bouldin removes the contents from 

eggs, which are then added to liquid media 

and cultured for the presence of Salmonella.

STEPHEN AUSMUS (D1337-11)

STEPHEN AUSMUS (D1336-6)
16 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

A research plot in Jonathan Dickinson State Park, with defoliated 

and browned clumps of Old World climbing fern, Lygodium 

microphyllum. The damage was caused by biocontrol caterpillars of 

the moth Neomusotima conspurcatalis, or Neo. Undamaged native 

ferns are shown in the foreground. 

ANTHONY BOUGHTON (D1349-1)

F

Tiny Moth Tackles Old World Climbing Fern 

ANTHONY BOUGHTON (D1455-1)

Neo

caterpillar 

feeding on a 

leaflet of L. 

microphyllum. 

or more than 12 years, ARS scientists and cooperators 

have been on a quest to control Old World climbing fern, 

one of the most invasive plants in all of Florida and a 

large threat to the prized Florida Everglades.

The fern, Lygodium microphyllum, can reach lengths 

of over 90 feet. It forms thick blankets of light-green vegetation 

that can completely cover other plants, blocking sunlight crucial 

to their survival. Lygodium also allows wildfires that would 

normally only scar cypress tree trunks to race up the tree and 

set the canopy afire.

If left uncontrolled, this aggressive invader could soon cover 

one-third of south Florida and cost $8 million annually in control 

expenses.

ARS entomologists Bob Pemberton and Anthony Boughton, 

with the Invasive Plant Research Laboratory in Fort Lauderdale, 

Florida, have been working closely with scientists from the 

Brisbane-based ARS Australian Biological Control Laboratory—

a cooperative venture with Australia’s Commonwealth Scientific 

and Industrial Research Organization, or CSIRO—to find natural 

enemies that will stop climbing fern’s spread. Additional cooperators include the South Florida Water Management District, 

the Florida Fish and Wildlife Conservation Commission, and 

the Florida Department of Environmental Protection’s Division 

of Recreation and Parks.

Now, they may have found a solution.

Small Insect, Big Job

A little moth known as Neomusotima conspurcatalis—nicknamed “Neo”—is currently the most successful of all the biocontrol agents that have been tested by the Fort Lauderdale and 

Brisbane scientists.

“Since its initial release in January 2008, Neo has rapidly 

expanded its populations,” says Pemberton. “There are hundreds 

of thousands of moths.”

Pemberton was the first to discover the biocontrol potential 

of Neomusotima insects. He found insects of this genus feeding 

on L. microphyllum near Hong Kong during a 1997 expedition. 
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 17

Later work by Brisbane scientists Matt Purcell, Tony Wright, former Brisbane director John Goolsby—now with ARS at Weslaco, 

Texas—and John Molden of the Department of Agriculture and 

Food, Western Australia, highlighted Neo’s potential. Rigorous 

testing by both labs led to Neo’s 2008 outdoor release in Florida.

Despite its small size, Neo is formidable. The moth reproduces quickly, generating large numbers of offspring almost 

every month. Neo’s larvae feed on Lygodium leaves and, in 

large numbers, can defoliate entire plants. The larvae also eat 

the later regrowth.

Today, Neo’s thriving colonies—direct descendants of the 

insects imported from Australia—prosper at three test sites in 

Florida’s Jonathan Dickinson State Park. Neo has browned and 

defoliated Lygodium at all three sites, according to Boughton, and 

is now expanding to adjacent Lygodium-infested areas in the park.

“Neo’s impact is incredible,” says Fort Lauderdale research 

leader Ted Center. “The involvement of the Australian lab was 

critical and shows the advantage of having ARS foreign labs.”

The push continues to find new insects—moths, mites, beetles, 

and more—to help hardworking Neo.

Why the need for more recruits?

Explains Pemberton, “Using a diverse array of organisms—

some feeding on the same parts of the fern and others feeding 

on different portions—provides a better attack on this weed.”

Stem Borers: Deadly Insiders

One of the most promising of the insects that might someday 

join the fern-fighting force in Florida is a small brown moth 

known as a “stem borer.” As its name implies, this biocontrol’s 

bailiwick is the elongated stems of climbing fern that extend 

upright from the plant’s dense, ground-hugging mats.

The female moth, which measures about a half-inch from 

wingtip to wingtip, lays eggs that hatch into unusually long, 

skinny, cream-colored larvae, explains entomologist Purcell, who is 

acting director at the Australian lab.

The larvae bore into the fern’s 

stems and, by eating the stem innards, or pith, create a snug home 

for themselves.

“This can be catastrophic for 

the plant,” says Purcell. “The stem 

borer’s tunneling and feeding can 

kill all of the fern’s growth above 

the larva’s entry point. That means, 

essentially, that a half-inch-long 

larva that bores a tunnel a few feet 

long has the potential to kill 40 feet 

or more of fern. That’s a remarkably powerful punch for so small 

an insect.”

Pioneering research by the Brisbane scientists pinpointed stem 

borers as potential biocontrols in 1999. Later expeditions taken 

by Purcell; CSIRO colleagues Tony Wright, Jeff Makinson, 

Bradley Brown, and Ryan Zonneveld; and former Brisbane 

director Goolsby encompassed Australia, Singapore, Thailand, 

Indonesia, Malaysia, and Hong Kong and other parts of China. 

These fern forays have yielded stem borers from several different 

species of Lygodium.

Preliminary determinations by M. Alma Solis, an expert on 

fern-feeding moths and research leader of the ARS Systematic 

Entomology Laboratory in Beltsville, Maryland, indicate that 

borers collected in Hong Kong, Singapore, and Thailand are 

actually new to science.

Notes Purcell, “We’re the most excited about the stem borer 

from Hong Kong because we’ve been able to raise it successfully 

in captivity in cages of potted Lygodium microphyllum plants.”

That hasn’t been the case, for instance, with the Singapore stem 

borer specimens. “They like thicker-stemmed plants which, at 

present, can’t be provided for them in the lab,” Purcell says. “That 

makes rearing the Singapore borers near impossible, for now.”

Robust laboratory colonies are a must. They’re essential for 

the “host-specificity tests” in which scientists determine whether 

stem borers can survive and reproduce on climbing fern exclusively, instead of being able to prosper on other plants—such 

as Florida’s many native ferns. And bustling lab colonies are of 

course needed to stock fern-infested Florida sites and to replenish those outdoor colonies until they become self-sustaining.

With further research and requisite federal and state approvals, 

stem borers may one day work in harmony with Neo to halt 

climbing fern’s advance. Their prospective new home, Florida’s 

fragile Everglades ecosystem, is an irreplaceable national 

treasure. If they help save the ’Glades, these insects will surely 

become a national treasure, too.—By Stephanie Yao and Marcia 

Wood, ARS.

This research is part of Crop Protection and Quarantine, an 

ARS national program (#304) described on the World Wide Web 

at www.nps.ars.usda.gov.

To reach scientists mentioned in this article, contact Stephanie 

Yao, USDA-ARS Information Staff, 5601 Sunnyside Ave., 

Beltsville, MD 20705-5129; phone (301) 504-1619, fax (301) 

504-1486, e-mail stephanie.yao@ars.usda.gov. X

ANTHONY BOUGHTON (D1454-1)

In Jonathan Dickinson State Park, entomologists Bob Pemberton 

(left) and Anthony Boughton inspect L. microphyllum vines that 

have been partly defoliated by Neo caterpillars. 

ANTHONY BOUGHTON (D1457-1)

Neo adults perched on 

leaflets of L. microphyllum.
18 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

swine influenza virus (SIV) surveillance 

pilot program. The goal is to better 

understand the epidemiology of SIV 

infections and to improve diagnostic tests, 

preventive management, and vaccines for 

swine and humans. This program has been 

instrumental in implementing surveillance 

for the 2009 outbreak, but it’s not the first 

time ARS influenza work has had major 

benefits. ARS scientists have been at the 

forefront of avian and swine influenza 

research for decades.

Agency scientists have developed tests 

to rapidly identify poultry infected with 

avian influenza and vaccines to protect 

against the disease. They’ve also developed and tested vaccines for swine. And 

ARS scientists have contributed to public 

health by identifying flu strains, assessing 

vaccines, and developing international 

Flu Fighters

Identifying, Treating, and Preventing 

the Flu With Help From ARS Research

standards for inactivating flu virus in 

cooked products.

Swine Surveillance

 A 2008 paper cowritten by ARS veterinary medical officer 

Amy Vincent states 

that swine influenza 

has undergone dramatic changes in the 

past decade, after 

nearly 80 years of 

relative stability. The 

increase in new subtypes and variants has 

complicated efforts 

to control the disease 

and increased the 

need for innovative 

strategies to fight it.

One such strategy 

is the pilot SIV surveillance program, 

in which APHIS 

coordinates with 

the National Animal 

Health Laboratory 

Network to screen 

potential SIV cases 

T

Transmission electron micrograph of the 

H1N1 virus.

CDC INFLUENZA LABORATORY (D1610-1)

ARS veterinary medical officers Kelly Lager (left) and Amy 

Vincent collect a nasal swab from a piglet to test for novel H1N1 

influenza virus. 

JAMES FOSSE (D1611-1)

he first reports of a novel swineorigin influenza outbreak surfaced 

in the U.S. media in April 2009. 

The U.S. Centers for Disease Control and Prevention (CDC) first 

detected human infection in mid-April. 

Over the next 6 weeks, human infections 

were detected in more than 40 countries 

and nearly every U.S. state.

Early media reports referred to the 

virus—now known as “2009 influenza A 

(H1N1)”—as “swine flu,” a potentially 

confusing term for the public. Scientists 

initially concluded that the virus came 

from pigs because its genetic material 

was most similar to that of swine influenza virus. We now know that the 2009 

H1N1 virus is a “triple reassortant virus,” 

meaning that it contains genetic material 

from swine, avian, and human influenza 

viruses—a mix that may help the virus 

spread quickly and pass between humans 

and pigs.

For some researchers, the story of a new 

influenza virus infecting pigs and people 

was all too familiar. As early as 2007, 

researchers from USDA’s Agricultural 

Research Service (ARS) and Animal and 

Plant Health Inspection Service (APHIS) 

had been monitoring a strain of influenza 

that could spread between pig and human 

populations.

In August 2007, several people developed flulike symptoms after exhibiting 

their swine at a county fair in Ohio. 

Many of the pigs became sick as well. 

Tests revealed the source of the illness: 

a triple reassortant influenza A (H1N1) 

very similar to viruses that are endemic 

in U.S. pig herds.

Scientists from ARS and APHIS characterized the virus and found that in pigs 

it was slightly more virulent than average. 

In light of the virus’s characteristics and 

its documented ability to spread from pigs 

to humans, the scientists advocated close 

monitoring of influenza in swine, birds, 

and other species.

In September 2008, ARS, APHIS, 

and CDC launched a collaborative effort 

funded by CDC to develop a national 
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 19

submitted from veterinary diagnostic 

laboratories. ARS then characterizes virus 

samples of special interest. The agencies 

also share virus isolates.

“We hope the pilot program will eventually become a permanent fixture,” 

Vincent says. “Having an established 

program would enable us to track not only 

where SIV occurs, but whether the virus 

undergoes significant mutations. This 

information could be essential in the event 

of an outbreak.”

The virus behind the current outbreak—

like the virus from the Ohio county 

fair—is a type of influenza A known as 

“H1N1.” Though these two viruses have 

some substantial genetic differences, they 

both have surface proteins from swine 

influenza viruses. The surface proteins of 

these viruses are very different from those 

of human seasonal influenza A (H1N1) 

viruses, which means that most humans 

do not have any cross-reactive antibody 

against them. Other viruses that have 

caused human illness, but originated in 

animals, include H5N1 and H7 viruses 

from poultry.

At the beginning of the 2009 H1N1 

outbreak in humans, pork producers had 

two important questions: Is the virus 

capable of infecting pigs? And if so, how 

will they respond? To find out, Vincent 

and her colleagues challenged young 

pigs with the virus in a biosafety level 

3 facility at the ARS National Animal 

Disease Center (NADC) in Ames, Iowa. 

They observed that the pigs developed 

clinical signs of influenza consistent with 

those seen in endemic SIV infections. The 

scientists are also examining antisera and 

existing vaccines to determine whether 

the immunity that develops in response to 

infection or vaccination will protect pigs 

against the current outbreak.

Pigs, Poultry, and Pathogenicity

Because the new 2009 H1N1 virus 

contains genetic material from avian 

influenza viruses, two more questions 

must still be addressed: Is the virus 

capable of infecting avian species? And 

are poultry and other birds potential 

vectors for influenza in humans? Though 

the answers to these questions are still 

unknown, ARS scientists have a strong 

foundation of avian influenza research on 

which to build.

Scientists at the ARS Southeast Poultry 

Research Laboratory (SEPRL) in Athens, 

Georgia, have developed and evaluated 

avian influenza vaccines, helped assess 

public health threats, evaluated virus virulence, and helped develop protocols for 

inactivating flu viruses in food products. 

More recently, they’ve been evaluating 

how specific viruses pass from one animal 

to another.

Domestic pigs generally catch influenza 

from other pigs, but they’re also susceptible to infection from humans and birds. 

Fortunately, several highly pathogenic 

strains of avian influenza virus don’t appear to cause significant disease in pigs. 

That’s the conclusion of a study led by 

Aleksandr Lipatov (now with the CDC). 

The research team also included Yong Kuk 

Kwon, Luciana Sarmento, Erica Spackman, David Suarez, and David Swayne at 

SEPRL, and Kelly Lager at NADC.

“The finding is significant because pigs 

are thought to be vessels for mixing avian 

influenza and human influenza to allow 

genetic reassortment that could set the 

stage for pandemic avian influenza,” says 

Swayne.

In the studies, piglets were exposed to 

four different strains of highly pathogenic 

H5N1 avian influenza viruses. Two swine 

influenza viruses were used as controls. 

The studies show that none of the H5N1 

virus strains caused significant or fatal 

disease in pigs, but they did cause mild to 

moderate inflammation in the lungs.

Infection with either swine influenza 

virus resulted in much more severe symptoms and pneumonia.

In related research, scientists at NADC 

and SEPRL have collaborated to develop 

two sets of diagnostic tests to quickly 

and accurately differentiate the new 2009 

H1N1 virus from endemic forms of swine 

and avian influenza viruses already circulating in the United States.

Research efforts like these are essential 

to ensuring the health and safety of people 

and livestock in the United States and 

around the world.—By Laura McGinnis 

and Sharon Durham, ARS.

This research is part of Animal Health, 

an ARS national program (#103) described 

on the World Wide Web at www.nps.ars.

usda.gov.

To reach scientists mentioned in this article, contact Laura McGinnis, USDA-ARS 

Information Staff, 5601 Sunnyside Ave., 

Beltsville, MD 20705-5129; phone (301) 

504-1654, fax (301) 504-1486, e-mail 

laura.mcginnis@ars.usda.gov. X

In studies to evaluate swine flu vaccines, 

cells are observed for signs indicating they 

are infected by live swine influenza A virus.

SCOTT BAUER (K11003-1)
20 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Closing In on a Citrus Killer

Huanglongbing, the Citrus Greening Disease

O

With the use of a transmission electron microscope, molecular biologist Jianchi Chen and 

technician Darlene Hoffmann, both with ARS in California, look for bacteria associated with 

citrus greening disease. 

STEPHEN AUSMUS (D1436-2)

of citrus—are conducting investigations 

that may yield new, affordable, ecofriendly ways to thwart this invasive 

disease and the psyllids that spread it.

Profile of a Pathogen and Its Vector

HLB causes afflicted citrus trees to 

weaken and eventually die. Death can 

result either from HLB itself or from other 

diseases to which the infection renders the 

citrus more susceptible.

As the disease progresses, leaves mottle 

and yellow, and tree growth is stunted. 

Infected trees produce either no harvest 

or low yields. The fruit may be lopsided, 

hard, bitter, and unmarketable.

HLB is generally thought to be caused 

by any of three different species of 

bacteria, namely, Candidatus Liberibacter 

africanus, americanus, or asiaticus. 

Psyllids such as the Asian citrus psyllid, 

Diaphorina citri, can become lifetime 

carriers of the disease soon after they 

feed on the sap of plants infected with 

the bacteria. However, the bacteria are 

harmless to the psyllids, as well as to 

people, pets, and livestock.

Growers can, of course, spray their 

orchards to kill the psyllids and can also 

destroy infected trees. But neither tactic is 

guaranteed to stop or wipe out the disease.

First detected in the United States 

in Florida in 2005, HLB has already 

infected millions of citrus trees in that 

state. The disease has recently shown 

up in Louisiana, and discovery of Asian 

citrus psyllids in Texas and California puts 

groves in these states at risk, too.

To Help Save Orchards, Test Psyllids!

Growers, nursery owners, and backyard 

gardeners who want to protect their prized 

citrus trees are hindered by the fact that 

there’s no way to reliably detect the HLB 

microbe early—well before the trees begin 

to show obvious symptoms.

But some diagnostic tests, though imperfect, have been developed. ARS plant 

pathologists Richard F. Lee and Keremane 

L. Manjunath and colleagues have taken 

one such test—intended for pinpointing 

the microbe in plants—and have adapted 

it to find the pathogen in psyllids. Lee and 

Manjunath are based at the ARS National 

Clonal Germplasm Repository for Citrus 

and Dates in Riverside, California.

Their test, though not the first for detecting Candidatus L. asiaticus in psyllids, is 

apparently one of the newest of its kind to 

be based on what’s known as “real-time 

qPCR” (quantitative polymerase chain 

reaction) technology.

The assay is comparatively quick 

and relatively inexpensive and can be 

performed by technicians working at any 

of the hundreds of labs across the country 

that already handle other PCR-based tests.

The scientists have used the test to 

analyze some 3,000 psyllids collected from 

orchards, backyards, retail nurseries, and 

other venues where citrus plants are grown 

or sold in Florida. The study showed, for 

the first time, that discount garden centers 

were likely involved in the inadvertent, 

ranges seem to have everything 

you’d ever want from an orchard-fresh fruit. This superstar 

citrus—one of America’s top-10 

favorite fruits—boasts a pleasing flavor, a cheerful color, and a healthimparting dose of vitamin C.

But a pair of powerful natural enemies 

is now making life difficult in some of the 

nation’s orange groves. One is a bacterium 

that causes a devastating, exotic disease 

known as Huanglongbing (HLB). The 

other is a tiny insect, a psyllid (pronounced 

SILL-id), that spreads the bacterium.

Oranges and many citrus relatives are 

extremely vulnerable to HLB. Also known 

as “citrus greening,” because infected 

oranges may remain green instead of ripening naturally, HLB is regarded as the 

world’s most destructive disease of citrus.

And HLB is incurable—at least for 

now. But ARS scientists in California and 

Florida—states that are leading producers 
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 21

Using a protein mass spectrometer, plant physiologist Hong Lin measures host plant gene 

expression in response to pathogen infection. 

STEPHEN AUSMUS (D1437-27)

widespread, and rapid progression of the 

disease throughout Florida in recent years. 

In particular, sale and transport of orange 

jasmine, or Murraya paniculata—a 

popular landscaping plant and citrus 

relative—may have played a surprisingly 

important role in the spread of the disease.

The research also demonstrated that 

assaying psyllids may provide a way to 

detect HLB as many as 2 years before 

disease symptoms become apparent in 

afflicted plants. Early detection gives 

plant-health officials, and others, a helpful 

heads up. No one wants a repeat of what 

happened in Brazil and Florida, where 

HLB apparently had a 5- to 10-year head 

start before it was detected.

Unmasking the Microbe’s Genetic 

Secrets

Meanwhile, other ARS scientists are 

working with collaborators in the United 

States and abroad to sleuth the genetic 

makeup, or genome, of Candidatus L. 

asiaticus. Their explorations may yield 

new clues to undermining the pathogen.

The work is particularly difficult because the microbe can’t be grown in 

pure culture in the laboratory. Such 

culturing would make it much easier 

for researchers to extract, evaluate, and 

decipher the sequence of the microbe’s 

genetic material, or DNA.

ARS plant physiologist Hong Lin, 

who is with the ARS San Joaquin Valley 

Agricultural Sciences Center near Parlier, California, has modified a technique 

known as “genome walking” to obtain the 

likely sequence of the microbe’s DNA. 

The approach has allowed his team to 

determine what sequences might occur 

on either the “upstream” or “downstream” 

ends of the very few stretches of 

Candidatus L. asiaticus DNA that have 

already been sequenced by researchers 

in Europe. Lin is using samples of DNA 

from HLB-diseased pummelo and other 

citrus in China.

In the south Florida city of Fort Pierce, 

plant pathologist Yong-Ping Duan and entomologist David Hall, both with the ARS 

U.S. Horticultural Research Laboratory, 

are using a different approach. Instead of 

studying DNA from infected citrus trees, 

they are studying DNA from psyllids that 

test positive for the microbe.

In comparing some of the predicted sequences from Duan’s research with those 

from the Parlier work, Lin has found a 

99-percent correlation. That’s impressive, 

given that the researchers are using different sources for the DNA, from different 

parts of the world, and are using different 

analytical techniques to sequence them.

Duan, who leads the Candidatus L. asiaticus genome sequencing work for ARS, 

has collaborated with Lin’s team in grouping the sequences into lengthy stretches. 

This piecing together has yielded a map 

of the complete genome of the microbe.

In California, Lin’s preliminary analyses 

have revealed interesting information 

about the microbe’s evolution and its 

relatedness to several other bacteria. 

These findings help broaden researchers’ 

knowledge of the little-known, HLBassociated Candidatus species.

In all, the citrus greening research is 

putting a powerful squeeze on microbe 

and psyllid alike.—By Marcia Wood,

ARS.

This research is part of Plant Diseases, 

an ARS national program (#303) described on the World Wide Web at www.

nps.ars.usda.gov.

Hong Lin is with the USDA-ARS San 

Joaquin Valley Agricultural Sciences Center, 9611 S. Riverbend Ave., Parlier, CA 

93648; phone (559) 596-2933, fax (559) 

596-2921, e-mail hong.lin@ars.usda.gov.

Yong-Ping Duan is with the USDA-ARS 

U.S. Horticultural Research Laboratory, 2001 S. Rock Rd., Fort Pierce, FL 

34945; phone (561) 462-5840, fax (561) 

462-5986, e-mail yongping.duan@ars.

usda.gov. X
22 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

ozone, a gas created when sunlight “cooks” 

automotive and industrial pollutants that 

originate from combustion of carbonbased fuels.

Levels of both gases are rising. The 

Intergovernmental Panel on Climate 

Change, an international panel of highly 

regarded scientists, estimates that CO2

levels could be about 1.5 times greater 

than the current 380 parts per million 

by 2050. The panel also estimates that 

daytime ozone in the summertime, now 

at about 50-55 parts per billion, may rise 

20 percent over the same period.

Besides assessing the effects of future 

air concentrations on both crops, the researchers are conducting a 5-year project 

to determine whether a widely accepted 

no-till cropping system will improve soil 

quality and sequester carbon when levels 

of the gases rise.

“We know no-till increases carbon 

sequestration in the soil. The question is, 

What is going to happen with elevated 

levels of CO2

, and how are changes in 

other atmospheric gases, namely ozone, 

going to affect that?” Booker says.

The Raleigh researchers have 16 opentop chambers, divided into 4 treatments: 4 

with elevated ozone, 4 with elevated CO2

, 

4 with both gases elevated, and 4 controls. 

They are pumping the chamber air with up 

to 40 percent more ozone and CO2

 than 

what is found in today’s ambient air. They 

are also charcoal-filtering the air so they 

can reduce ozone in the control chambers 

and tease out the impact that different 

ozone and CO2

 levels, by themselves, have 

on the plants.

In addition, the researchers are putting 

the postharvest residues, such as plant 

stems, empty pods, and dead leaves, 

back into the chambers, essentially 

G lobal greenhouse gas emissions 

are projected to rise dramatically 

in the next 40 years, with increased 

outputs of carbon dioxide (CO2

) 

being the main culprit. In light of 

our changing environment, Agricultural 

Research Service scientists in Urbana, 

Illinois, and Raleigh, North Carolina, are 

examining how the increase in greenhouse 

gases, particularly CO2

 and ozone, will 

affect two of the world’s most widely 

planted crops: soybeans and wheat.

Open-Top Chambers Offer Insight

At the Plant Science Research Unit in 

Raleigh, ARS plant physiologists Fitzgerald Booker, Kent Burkey, and Ed Fiscus 

are assessing how climate change will 

affect soybean and wheat growth rates, 

crop yield, and soil chemistry by exposing 

the crops to the elevated levels of CO2

 and 

ozone projected for the year 2050.

Soybeans, wheat, and other crops 

grow more when CO2

 levels are elevated, 

because there is more carbon captured 

during photosynthesis for the plants to use. 

But those same plants are damaged and 

stunted by elevated levels of ground-level 

Soybean & 

Wheat 

Response 

to Climate 

Change

ARS scientists Carl Bernacchi (left), Don Ort (center), and Lisa Ainsworth in a plot of 

soybeans treated with elevated carbon dioxide (CO2

) at the SoyFACE Global Change 

Research Facility at the University of Illinois Research Farm in Urbana. In the foreground 

is an automatic retractable awning used to capture rainfall in order to investigate the 

interaction of drought and elevated CO2

 on soybean. Behind the scientists is an array 

of infrared heaters used to raise the temperature of a portion of the plot to investigate 

interactions with anticipated global warming. 

INSTITUTE FOR GENOMIC BIOLOGY/UNIVERSITY OF ILLINOIS (D1546-2)

PEGGY GREB (D1548-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 23

making them small, self-contained plots 

that mimic conditions found in no-till 

systems. To measure changes in the soil’s 

carbon and nitrogen content makeup, the 

researchers take samples twice a year. 

The CO2

 pumped into the chambers has a 

specific isotope marker so they can track 

it from the air through the plants and into 

the soil. They are analyzing the soil cores 

by depth to determine where composition 

changes may occur and also the amount 

of bacteria and fungi found in each layer 

to see whether microorganism populations 

or communities change.

After completing 3 years of the project, 

preliminary results show a trend for 

higher levels of soil carbon in chambers 

with elevated CO2

 but not in chambers 

with elevated ozone. Elevating CO2

 also 

reduced protein levels in wheat flour by 7 

percent to 11 percent, but it had no effect 

on soybean seed protein.

SoyFACE: New Technology, New 

Understanding

Researchers in Urbana and cooperators 

with the University of Illinois at UrbanaChampaign have been working on a project 

called “SoyFACE”—short for Soybean 

Free Air Concentration Enrichment—that 

also measures how the projected increases 

in CO2

 and ozone will affect soybean 

production.

FACE technology, which was first 

used for crop research by ARS soil scientist Bruce Kimball, ARS plant physiologist Jack Mauney (now retired), and 

scientists from the U.S. Department of 

Energy’s Brookhaven National Laboratory, allows testing of plants in open-air 

field conditions. ARS scientists Don Ort, 

Lisa Ainsworth, and Carl Bernacchi, in 

the Photosynthesis Research Unit, and 

Randall Nelson, in the Soybean/Maize 

Germplasm, Pathology, and Genetics Research Unit, use the technology to produce 

atmospheric conditions predicted for the 

year 2050. 

Horizontal pipes arranged in an octagon 

about 70 feet in diameter surround each 

test plot. A computer measures wind direction and speed, then releases concentrated 

amounts of CO2

 and ozone. The wind 

carries the gases across the soybean crop.

“At the start of the project, we sought 

to understand how CO2

 and ozone affect 

soybean independently,” says Ort. “We 

found soybean yield increases by about 12 

percent at the elevated CO2

 concentrations 

predicted for 2050, half of what previous 

studies estimated. We also found that 

increased ozone is quite harmful to yield, 

reducing it by about 20 percent. In fact, 

our study showed current levels of ozone 

are already suppressing soybean yield by 

up to 15 percent.”

The results of the individual studies led 

the scientists to examine the combined 

effects of CO2

 and ozone on soybean. 

They found that elevated CO2

 partially 

offsets the ozone damage. These findings 

with SoyFACE confirm general results 

obtained with open-top chamber studies of 

ozone and CO2

 effects on crop yield conducted at Raleigh and other locations. But 

the ability of SoyFACE technology to test 

these principles in the open air, without the 

environmental modifications caused by 

the chambers themselves, means greater 

confidence in our understanding of how 

plants respond in the real world, including the actual estimates of impact on crop 

yields. Furthermore, there is much to be 

learned about how other interacting factors 

that affect ozone uptake may come into 

play by mid-century.

The scientists recently began studying 

how combined factors will affect soybean 

production. They are looking at drought 

and increased temperature, drought and 

increased CO2

, and elevated temperature 

and CO2

. They’ll also be analyzing how 

microbial communities and soil carbon 

storage are affected by these changes.

These projects provide valuable information that will help breeders develop 

soybean cultivars better adapted to an 

ever-changing climate.—By Stephanie 

Yao and Dennis O’Brien, ARS.

This research is part of Air Quality 

(#203), Global Change (#204), and Plant 

Biological and Molecular Processes 

(#302), three ARS national programs described on the World Wide Web at www.

nps.ars.usda.gov.

To reach scientists mentioned in this 

article, contact Stephanie Yao, USDA-ARS 

Information Staff, 5601 Sunnyside Ave., 

Beltsville, MD 20705-5129; phone (301) 

504-1619, fax (301) 504-1486, e-mail 

stephanie.yao@ars.usda.gov. X

Plant physiologist 

Fitzgerald Booker 

prepares to place 

an optical scanner 

into a tube that will 

be positioned in the 

soil to photograph 

soybean roots. 

The photos will 

be analyzed to 

determine changes 

in root length and 

distribution caused 

by exposure to 

elevated carbon 

dioxide and ozone, 

which are pumped 

into the open-top 

field chambers. 

To assess oxidative stress in soybean 

grown at SoyFACE under elevated ozone 

concentrations, ARS molecular biologist 

Lisa Ainsworth (back) and graduate student 

Kelly Gillespie use a liquid-handling robot 

to perform a high-throughput assay. 

PEGGY GREB (D1550-1) 

DEALING WITH

CLIMATE CHANGE
24 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

t takes around 5 weeks for a tiny 

watermelon flower to grow into a 

ready-to-eat watermelon. Though 

ripe watermelons typically weigh 

anywhere from 5 to 40 pounds, 

record-breakers have tipped the 

scales at 250 pounds or more.

“Watermelon is a fruit that grows so 

fast, and it can get so big,” says ARS 

plant geneticist Amnon Levi. “We know 

there must be some very interesting genes 

at work.”

Levi works at the ARS U.S. Vegetable 

Laboratory in Charleston, South Carolina. 

He teamed up with plant pathologist Pat 

Wechter and plant geneticist Karen Harris 

on the first-ever study that identified and 

characterized key genes regulating watermelon growth and development.

Over a 3-year period, plant geneticist 

Angela Davis, who works at the ARS 

South Central Agricultural Research 

Laboratory in Lane, Oklahoma, grew 

watermelons in the field for the research to 

ensure that the genes would be responding 

to actual field conditions, such as pathogens and weather extremes.

“One year it was so dry that we had to 

stop watering because water restrictions 

had been imposed,” Davis notes. “The 

other 2 years it rained so much that the 

plants became stressed from too much 

water.”

Davis extracted RNA from watermelon 

fruit at three stages of growth and ripening: at 12 days after pollination (DAP), 

when the flesh was white; at 24 DAP, 

when the flesh was pink; and at 36 DAP, 

when the flesh was red. Then she sent 

RNA from the tissue samples to Charleston for analysis. 

Genes Prompt Plus-Size Fruit

Levi used this collection of RNA to 

develop a library of 832 expressed sequence tags (ESTs), which are unique 

gene segments that direct different aspects 

of development and metabolism. Then he 

worked with Wechter and Harris to decipher how the ESTs regulated plant growth 

and development.

Genes for Giants

Why 

Watermelons

Just Grow and I Grow

Plant pathologist Pat Wechter (left) and plant geneticist Amnon Levi examine watermelon for 

fruit quality. They are studying gene expression in the three stages of watermelon ripening. 

The team found that these ESTs were 

active in metabolism, cell growth, cell 

development, and transporting nutrients 

and other substances across cell walls. 

They also came into play in cell division, 

cellular communication, DNA copying, 

plant defense, and stress response.

The Charleston researchers then identified significantly different levels of EST 

expression during the early, middle, and 

late stages of fruit growth and ripening. 

They found 335 ESTs that had at least 

PEGGY GREB (D1432-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 25

central component of the ripening process. 

And if it’s important in watermelon, it 

could be important in other nonclimacteric 

fruit as well.”

Jim Giovannoni is a molecular biologist 

who works at the ARS Robert W. Holley 

Center for Agriculture and Health in 

Ithaca, New York. He maintains the 

Cucurbit Genomics Database (www.icugi.

org), a gene bank for the Cucurbitaceae 

family that is used by researchers around 

the world. He helped the Charleston team 

sort through the watermelon ESTs.

“Finding ethylene activity in watermelon is significant because it shows the 

existence of the same type of genes that 

are also found in tomato and Arabidopsis—our model plant,” Giovannoni says. 

“This shows that genes involved in model 

systems are also seen in crop systems, 

which validates the models we use. In addition, we have identified ESTs that could 

be used to develop molecular markers for 

ethylene response in watermelon.”

Enigmatic ESTs Remain

Though the ESTs linked to ethylene 

activity were a surprise, the team was able 

to pinpoint their function. But the team 

also found 96 ESTs that remain somewhat 

of a mystery.

“They appear to be active all the time, 

which suggests they regulate more generalized, basic functions for plant survival,” 

Wechter says. “But we can’t match them 

up with any other known plant ESTs. 

We’re trying to confirm they are unique 

to watermelon.”

In 2008, U.S. watermelon crops valued 

at $492 million were planted on just 

over 134,000 acres. But pathogens—

including watermelon vine decline and 

Phytophthora blight—continue to threaten 

production. Finding sources of genetic 

resistance to these threats is essential to 

the success of watermelon crops across 

the southern United States.

“Cultivated watermelons are not genetically diverse at all, which makes them 

much more vulnerable to pathogens and 

environmental stresses,” Harris notes. “It’s 

difficult to find genetic differences in such 

a narrow selection of cultivars.”

“I want to do more studies looking at 

the interaction of watermelon genes when 

the plant is challenged by pathogens,” 

Wechter adds. “Our EST study is a good 

start. Now we need to build on this information and find ways to develop more 

resistant melons to meet the challenges in 

field production.”—By Ann Perry, ARS.

This research is part of Plant Genetic 

Resources, Genomics, and Genetic Improvement (#301) and Plant Diseases 

(#303), two ARS national programs described on the World Wide Web at www.

nps.ars.usda.gov.

To reach scientists mentioned in this 

article, contact Ann Perry, USDA-ARS 

Information Staff, 5601 Sunnyside Ave., 

Beltsville, MD 20705-5129; phone (301) 

504-1628, fax (301) 504-1486, e-mail 

ann.perry@ars.usda.gov. X

a twofold increase or decrease in copy 

number in at least one of the three stages. 

Of these 335 ESTs, 239 were very similar 

to ESTs found in other plants, while the 

remaining 96 had not been previously 

identified in any sequenced plant species.

“Most of these genes regulate targeted 

activities,” Wechter says. “They are very 

specific genes that do certain things at a 

certain time during growth and ripening. 

Many of them are involved in the development of the watermelon vascular system, 

which is a crucial component for growth 

and ripening.”

“The vascular system in a watermelon 

forms very fast because it is building 

the infrastructure for fruit, like building 

a highway before building a city,” Levi 

says. “This system is how fluids transport 

sugars from the leaves into the fruit.”

Ethylene Enters the Picture

But some of the results were unexpected—and may someday give breeders and 

producers an edge in moving watermelons 

to market.

In some types of fruit, ethylene gas 

is produced, and it is responsible for 

many ripening processes. These fruits 

are referred to as “climacteric fruits.” In 

fact, producers often harvest climacteric 

fruits—such as tomatoes—before they 

are ripe, and then promote ripening by 

exposing the harvested fruit to ethylene.

But ethylene has not been linked to 

ripening of nonclimacteric fruits. Scientists consider watermelons and other 

cucurbits—along with grapes, citrus, and 

strawberries—to be nonclimacteric fruits. 

So Wechter and the others were very 

surprised to see differences in expression 

levels of genes involved in ethylene 

production in watermelon fruit. They 

then measured the amount of ethylene 

produced by developing and ripening fruit. 

They found a burst of ethylene production 

during the white-fruit stage and lesser 

amounts produced during the later stages.

“We just didn’t think ethylene had 

any role in the ripening of watermelon,” 

Wechter says. “Now we know it could be a 

Plant geneticist Karen Harris removes 

watermelon flesh for RNA extraction. 

PEGGY GREB (D1433-1)
26 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Using Floating Vegetated Mats To Treat 

Fishery Wastewater

Of the plant species tested on floating mats in fishery wastewater, 

iris plants, shown here, grew best.

Soil scientist Robert Hubbard adjusts iris plants recently 

transplanted onto floating mats in aquaculture tanks. The tanks 

have been sprigged with different plant species to see which plants 

grow best in fishery wastewater. The leafy green plants in the back 

are canna lilies. 

BOBBY SHIVER (D1291-1)

ROBERT HUBBARD (D1292-1)

S

“Our first 

objective is to 

find plant species that grow 

well in fishery 

wastewater.”

—Robert Hubbard

aving water is an environmentally responsible goal, especially in the southeastern parts of the country, where 

droughts are fairly frequent. To that end, Agricultural 

Research Service scientists in Tifton, Georgia, are testing the feasibility of using floating vegetation to remove 

nutrients from fishery wastewater. The long-term goal 

is to develop a system to treat fishery wastewater, return it to 

ponds for reuse, and use the nutrients to produce biomass, or 

plant material.

The study participants are soil scientist Robert K. Hubbard, at 

the ARS Southeast Watershed Research Laboratory; plant geneticist William Anderson and plant pathologist Jeffrey P. Wilson, at 

the ARS Crop Genetics and Breeding Research Unit, in Tifton; 

and University of Georgia animal science associate professors 

Gary Burtle and Larry Newton.

The current study is being conducted jointly by ARS and the 

University of Georgia’s Aquaculture Unit in Tifton. “It builds 

on previous research showing that vegetation 

can be grown on floating mats in swinewastewater lagoons,” says Hubbard.

Wastewater from the fish-production ponds 

is pumped into 340-gallon aquaculture tanks. 

Each tank has a 10-foot-square floating mat 

on which the vegetation grows. “Our first 

objective is to find plant species that grow 

well in fishery wastewater,” says Hubbard.

The researchers are currently testing 12 

different plant species: St. Augustinegrass, 

Tifton 85 bermudagrass, common bermudagrass, canna lilies, iris, bamboo, bulrush, 

cattail, bordergrass, napiergrass, reeds, and 

maidencane. “So far, the iris is the best performer,” says Hubbard.

In the second part of the study, beginning in spring 2009, 

researchers will determine the effects of the vegetation on water 

quality and the amount of nutrients removed when plant biomass 

is harvested, Hubbard says.

The plant material will be harvested on an as-needed basis 

and the plant tissue analyzed for nitrogen, phosphorus, and 

potassium. Harvested plant material has several potential uses. 

It can be transplanted, used as feedstock for energy production, 

or composted and used as a soil amendment.—By Sharon 

Durham, ARS.

This research is part of Soil Resource Management (#202), 

and Manure and Byproduct Utilization (#206), two ARS national 

programs described on the World Wide Web at www.nps.ars.

usda.gov.

Robert K. Hubbard is at the USDA-ARS Southeast Watershed 

Research Laboratory, 2316 Rainwater Rd., Tifton, GA 31793; 

phone (229) 386-3893, fax (229) 386-7215, e-mail bob.

hubbard@ars.usda.gov. X
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 27

have a trap in place for a long time and you 

don’t want to have to check it every week 

or two,” says Mankin, at the ARS Center 

for Medical, Agricultural, and Veterinary 

Entomology in Gainesville.

Armed with automated traps, managers 

could improve the timing and placement of 

control measures or even avoid using them 

when there’s no need. The researchers’ 

insect intelligence gathering isn’t restricted 

to stored-product pests, though. They’re 

also targeting home intruders like Blattella germanica (the German cockroach) 

and Cimex lectularius, better known as 

the “bed bug.”

Mankin says their objective was to create a device that would make automated 

insect monitoring not only affordable, but 

also easy to use and reliable. Toward that 

end, they integrated commercially available sensors (LEDs, microphones, and 

piezoelectric film) with high-gain amplifiers and laptop-run software for analyzing 

digital signals.

Their system uses the sensors to collect 

infrared, acoustic, and vibrational signals 

generated by three kinds of insect movements: wriggling, crawling, and scraping. 

The software analyzes the signals to create 

a profile of the target insect that distinguishes it from other species.

The researchers tested their device on 

three stored-product pests (rice weevil, red 

flour beetle, and drugstore beetle) and two 

household pests (German cockroach and 

bed bug). Individuals of each pest were 

placed inside small arenas where their 

signals could be collected and analyzed 

for differences in profile, magnitude, and 

duration. Although all five species generated all types of signals, red flour beetles 

mostly wriggled, German cockroaches 

typically ran or crawled, and bed bugs 

mostly scraped.

Mankin envisions users placing the devices in traps in or near infested structures 

and monitoring them remotely via laptop 

computer. “You would probably receive an 

alarm when a potential target insect was 

detected,” he says. “The information could 

also be saved in a spreadsheet, with the time 

of occurrence and probability that this was 

a target insect.”—By Jan Suszkiw, ARS.

This research is part of Crop Protection 

and Quarantine, an ARS national program 

(#304) described at www.nps.ars.usda.gov.

Richard Mankin is in the USDA-ARS 

Insect Behavior and Biocontrol Research 

Unit, Center for Medical, Agricultural, and 

Veterinary Entomology, 1700 S.W. 23rd 

Dr., Gainesville, FL 32608; (352) 374-

5774, richard.mankin@ars.usda.gov.*

Grain elevators, warehouses, and 

food-processing facilities are 

a hungry insect’s delight, 

thanks to ample food and 

climate-controlled conditions. Fortunately, 

there are many effective strategies for 

keeping stored-product insects in check—

including targeting of problem areas with 

extra sanitation measures and baits. But 

determining pest whereabouts and numbers 

in order to effectively implement these 

strategies can be challenging.

Now, after 8 years of research, Agricultural Research Service entomologist 

Richard Mankin and colleagues may 

have some inexpensive help. Using commercially available parts, they’ve built a 

monitoring device that detects insects by 

the sounds they make. 

Collaborating with Mankin are North 

Carolina State University researchers Ryan 

Hodges, Troy Nagel, and Coby Schal, all 

in Raleigh; and Roberto Pereira and Philip 

Koehler, both at the University of Florida 

in Gainesville.

The most likely application will be to 

automate routine monitoring of industrialscale traps, especially those placed in hardto-reach areas like crawl spaces or near 

food-processing equipment. “Automation 

could be useful in a situation where you 

PEGGY GREB (D2123-1)

Entomologist Richard 

Mankin examines 

signals collected by an 

inexpensive prototype 

system (on the bench, 

at his fingertips) 

for automated 

insect detection and 

identification.

Entomologist Richard 

Mankin examines 

signals collected by an 

inexpensive prototype 

system (on the bench, 

at his fingertips) 

for automated 

insect detection and 

identification.

New Device Eavesdrops on Insect Pests
28 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

For almost 10 years, Agricultural Research 

Service (ARS) soil scientists Matias 

Vanotti and Ariel Szogi have worked with 

farmers, state agencies, and businesses to 

improve swine manure management practices. Now the scientists have developed a 

streamlined system that delivers a winning 

trifecta—healthier pigs, healthier profits, 

and a healthier environment.

A key factor in this success? “We paid 

lots of attention to what farmers and 

industry were telling us,” says Vanotti, 

who works with Szogi at the ARS Coastal 

Plains Soil, Water, and Plant Research 

Center in Florence, South Carolina.

Manure can be used to fertilize crops, 

but excess nitrogen and phosphorus that 

is not taken up by plants can be carried 

away by water and end up polluting nearby 

streams, lakes, and groundwater. Controlling pathogens, odors, and emissions of 

ammonia and greenhouse gases is also 

a concern with livestock production. So 

swine producers in North Carolina—who 

in 2008 sent close to 20 million pigs to 

market—are always on the lookout for 

ways to reduce the environmental impact 

of their facilities.

Vanotti and Szogi have been essential 

partners in this search. In 2005 they 

unveiled a first-generation swine manure 

management system created in partnership with Terra Blue, Inc., a private 

business based in Clinton, North Carolina. 

(See “Blue Lagoons on Pig Farms?” 

Agricultural Research, March 2005.)

Taking It to the Next Level

When Vanotti and Szogi started out, the 

technology available to them resulted in a 

highly effective first-generation treatment 

system. But the results from their farmscale trials and new discoveries suggested 

that they could design an even more economical and simple process.

An added incentive: In 2007, the State of 

North Carolina started a statewide Lagoon 

Conversion Program (LCP) that provided 

financial support to livestock farmers who 

installed new manure management technologies that improved water and air qual

ARS soil scientists Matias Vanotti (left) and Ariel Szogi (right) and Lewis Fetterman, the CEO of Terra 

Blue, Inc., examine swine wastewater before (dark liquid) and after (clear liquid) treatment in the 

second-generation system they invented.

PEGGY GREB (D1774-1)

Producers and Pigs Profit From Manure 
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 29

 Management Process

Close-up of piglet and sow.

ity. The LCP set clearly defined targets for 

techniques that would meet their criteria of 

an Environmentally Superior Technology 

(EST) for manure management.

An EST needed to eliminate discharge 

of animal waste to surface waters and 

groundwater. It also needed to “substantially eliminate” emissions of ammonia and odors detectable beyond the 

production facility. An EST would also 

substantially eliminate the release of 

disease-transmitting vectors and pathogens as well as nutrient and heavy metal 

contamination of soil and groundwater. 

And an EST would need to run economically and efficiently. 

The scientists’ system already met the 

environmental targets. “We needed to 

demonstrate that we could cut costs while 

maintaining the efficiency of the firstgeneration system,” Szogi says.

So Vanotti and Szogi went back to the 

drawing table and worked with Lewis 

Fetterman, the chief executive officer of 

Terra Blue, Inc., to redesign and fine-tune 

the process. In the end, the team made 24 

changes to the first-generation system to 

lower its installation and operating costs 

and improve its reliability.

A U.S. Patent was granted for this new 

system (U.S. Patent 7,674,379, March 9, 

2010).

The on-farm system used solid-liquid 

separation and nitrogen and phosphorus 

removal processes. In the right combination, these systems replaced traditional 

anaerobic lagoon systems with a process 

that produced clean, deodorized, and disinfected effluent.

After processing, the nutrient-rich solids were transported off-site to a central 

composting facility that produced class A 

composted materials for making organic 

plant fertilizer and plant growth media.

The team reduced the solid-liquid separation operation from 7 days a week to just 

2. Several other adjustments were also 

made to this process, including simplifying the equipment used in the dewatering 

process and the production of drier solids. 

This improved solids handling, lowered 

transportation costs, and made the solids 

more suitable for composting. It also increased their potential for use as fuel for 

on-farm energy generation by thermal 

technologies.

To cut costs further, Vanotti and Szogi 

removed two tanks from the biological 

nitrogen removal process and incorporated 

a high-performing nitrifying bacterial 

sludge (HPNS), which they developed 

over 10 years in the laboratory. The new 

HPNS was well adapted to operate efficiently in both high-ammonia wastewater 

and cold temperatures, which translated 

into a smaller plant footprint. It also reduced the cost of ammonia removal. 

A U.S. Patent Application was filed for 

the HPNS (Serial No. 12/495,958, July 

1, 2009).

Finally, the scientists invented a simplified process to simultaneously separate the 

phosphorus and the manure solids. This 

innovation required fewer polymers than 

the previous separation system and also 

reduced equipment costs.

The revamped system was tested for 

15 months on a 5,145-head swine farm 

over 4 growing cycles. For this full-scale 

project, they collaborated with microbiologist Patricia Millner, who works at the 

ARS Environmental Microbial and Food 

Safety Laboratory in Beltsville, Maryland, 

Using a deep sampling probe, Ariel Szogi inspects the amount of calcium phosphate produced in 

a phosphorus-separation module that is part of the new system.

PEGGY GREB (D1777-1)

and chemist John Loughrin, who works at 

the ARS Animal Waste Management Research Unit in Bowling Green, Kentucky.

The results: the revamped system met 

EST standards at one-third the cost of the 

previous version. In cleaning up manure 

wastewater, the system removed almost 

100 percent of pathogens and odorcausing components, 95 percent of total 

phosphorus, 97 percent of ammonia, and 

more than 99 percent of heavy metals 

copper and zinc.

The new system also cut emissions of 

methane and nitrous oxide—powerful 

greenhouse gases—by 97 percent. In addition, the system transformed the old lagoon into an aerobic reservoir that reduced 

90 percent of the ammonia emissions.

The second-generation system used 

less energy to boot—power consumption 

dropped by 44 percent. The newer system 

was also more labor efficient and easier 

to operate than the first system, in part 

because of the development of operation 

practices that integrated automation with 

simple operator input.

SCOTT BAUER (K7623-1)
30 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

After processing, the nutrient-rich solids are transported off-site to a centralized composting facility. 

The composting process results in materials with an earthy scent and rich texture that can be used 

in organic fertilizers, soil amendments, and potting soils.

Matias Vanotti and C. Ray Campbell, vice 

president of research and development, Terra 

Blue, Inc., examine a compost sample.

Payback Time

All told, the second-generation technology was two-thirds less expensive to build 

and operate than the first system. What 

Vanotti and Szogi didn’t anticipate is how 

well the animals would respond.

But Billy Tyndall, the farmer who 

owned the facility where the secondgeneration system was being tested, began 

to notice an improvement in his pigs immediately after the system was installed. 

“The animals were heavier,” Szogi says. 

“And they were showing a better conversion of feed.”

The scientists and Tyndall were so 

impressed that they extended the project—originally planned for 5 months—to 

run for another year and a half to see if the 

results stayed consistent over five growing cycles. At the end of the study, the 

scientists tallied up the surprising results.

Daily weight gain increased 6.1 percent, 

and feed conversion improved 5.1 percent. 

Animal mortality decreased 47 percent, 

and cull weight was reduced 80 percent. 

The farmer sold an average of 5,265 pigs 

per growing cycle, which resulted in a 

1,138,247-pound net gain per cycle. Using the second-generation system instead 

of the lagoon system, the farmer sold 

61,400 pounds more hogs—a 5.8 percent 

increase—per growing cycle.

“Participating in the program took my 

average farm to the top of the field,” Tyndall declares.

The scientists attribute the productivity improvement in part to the improved 

air quality and health conditions in the 

barns. Since the recycled wastewater was 

mostly ammonia free, ambient ammonia 

levels in the barns dropped an average of 

75 percent.

“Improvement in animal production is 

important to farmers because that’s their 

bottom line,” Vanotti says.

Fetterman, their Terra Blue, Inc., partner, sees it from another angle. “If you 

treat the pigs well, they will pay you 

back,” he says.

Sharing the Success

The second-generation system was 

discussed in a chapter of “Manufacturing 

Climate Solutions: Carbon-Reducing 

Technologies and U.S. Jobs,” published 

in 2008 by Duke University. The report 

was commissioned by the AFL-CIO and 

the Environmental Defense Fund and 

featured technologies that could help 

reduce greenhouse gas emissions and 

create green jobs in the United States. 

The authors concluded that the secondgeneration system could help swineproducing states protect existing jobs 

and keep the door open for future job 

expansion.

In 2009, the USDA Natural Resources 

Conservation Service’s Environmental 

Quality Incentives Program began a 5-year 

initiative with additional funding for North 

Carolina livestock farmers who participate 

in the LCP. At the time the program was 

established, only the second-generation 

system met all the LCP qualifications 

for funding, which will pay for up to 90 

percent of the costs involved in installing 

an EST for manure management.

“When one considers the many direct 

and indirect benefits of the cleaner hogwaste technology, farmers and society may 

not be able to afford not to convert to the 

new technologies,” Fetterman observes.

“We learned our lessons and tried to 

make a new system as simple to operate 

and economical as possible,” Vanotti adds. 

“Now we need to install these systems in 

a sufficient number of farms to confirm 

their environmental benefits at a regional 

scale and to facilitate the development of 

markets for co-products from recovered 

manure nutrients.”—By Ann Perry, ARS.

This research is part of Manure and 

Byproduct Utilization (#206), Water 

Availability and Watershed Management 

(211), and Food Safety (#108), three ARS 

national programs described at www.nps.

ars.usda.gov.

Matias B. Vanotti and Ariel A. Szogi are 

with the USDA-ARS Coastal Plains Soil, 

Water, and Plant Research Center, 2611 

W. Lucas St., Florence, SC 29501-1242; 

phone (843) 669-5203, ext. 108 [Vanotti], 

(843) 669-5203, ext. 109 [Szogi], matias.

vanotti@ars.usda.gov, ariel.szogi@ars.

usda.gov. *

 PEGGY GREB (D1778-1) PEGGY GREB (D1779-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 31

The coconut tree is a symbol of the Tropics, and as a source of 

fiber, food, fuel, soap, and cooking oil, it is sometimes called 

“the tree of life.” But one aspect of the tree has remained a mystery—its origins. Scientists have debated the tree’s genealogical 

roots for decades.

 Using genetic markers found in coconuts and other palm 

trees from around the world, Alan Meerow, a geneticist with the 

USDA-ARS Subtropical Horticulture Research Station in Miami, 

Florida, has completed a phylogenetic analysis of a large group 

of palm species (the Attaleinae subtribe) that provides the most 

comprehensive look yet at the coconut tree’s family history. The 

results suggest that the ancestors of the coconut tree originated in 

South America, that the tree’s closest living relatives are a modern 

genus of American palms (the genus Syagrus), and that it diverged 

from them about 35 million years ago. The genus Syagrus includes 

another popular Florida ornamental, the queen palm.

Meerow and colleagues also found that the modern coconut 

tree probably evolved about 11 million years ago, perhaps in 

the South Pacific. The Fiji Dwarf, a variety of coconut tree now 

grown in the United States, shares its South Pacific ancestry with 

many of today’s other coconut varieties, according to Meerow. 

“The Fiji Dwarf is more distantly related to all these other varieties,” he says.

The work, published in PLoS One, is more than an academic 

exercise. Five of the 80 known varieties of coconut tree are major 

ornamentals in Florida. Identifying their closest relatives will help 

in the search for genes with traits capable of resisting diseases, 

insect pests, and other threats. An epidemic of lethal yellowing 

phytoplasma in the early 1980s destroyed an estimated 100,000 

coconut palms in South Florida. Bud rot, caused by several fungal 

pathogens, threatens coconut production around the world.

“The more we know about it, the easier it will be to address 

future threats,” Meerow says.

Patterns of differences in DNA can open a window into a plant’s 

evolutionary past, revealing when it diverged from its ancestors. 

Meerow and colleagues looked for patterns among a family of 

genes developed as markers by ARS researchers studying cacao 

(chocolate) plants. Known as “WRKY genes,” they are valuable 

“clocks” for dating the occurrence of important evolutionary 

events.

With these molecular clocks and evidence from fossil palms, 

Meerow traced the coconut tree’s ancestry back more than 40 

million years to palms that grew in both Madagascar and eastern 

Brazil. He also found that milestones in the coconut’s early “family tree” coincide with major geological events in South America, 

making it likely they played a role in how these palms evolved. 

A group of palm species in southern Brazil, for example, split off 

from a relative in Chile about 14 million years ago, around the 

time when geological events gave rise to the Andes Mountains. 

The extensions of oceans into the western Amazon region that 

lasted from 25 to 30 million years turned dry areas into wetlands 

and probably altered the evolution of coconut ancestors growing 

at the time across South America, Meerow says.—By Dennis 

O’Brien, ARS.

This research is part of Plant Genetic Resources, Genomics, 

and Genetic Improvement, an ARS national program (#301) 

described at www.nps.ars.usda.gov.

 Alan W. Meerow is with the USDA-ARS Subtropical Horticulture Research Station, 12501 Old Cutler Rd., Miami, FL 33158; 

(786) 573-7075, alan.meerow@ars.usda.gov. *

The coconut variety Niu Leka, or Fiji Dwarf (see back cover), from 

the South Pacific may represent the earliest lineage in the coconut’s 

domestication. 

A SYMBOL 

OF THE 

TROPICS

Unraveling the 

Origins of
32 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

eanuts are an important crop, 

contributing more than $4 billion 

to the country’s economy each 

year. But rapid growth in cities 

along with water level declines 

in aquifers throughout the South have 

resulted in fewer acres for farming and 

less water available for irrigation. To meet 

future food-supply demands, crop production will have to increase, but it must do 

so under the constraints of less water and, 

most likely, less farm land.

Agricultural Research Service scientists 

with the Plant Stress and Germplasm 

Development Research Unit in Lubbock, 

Texas, and the National Peanut Research 

Laboratory (NPRL) in Dawson, Georgia, 

are working with cooperators to help peanut farmers maintain and improve their 

production in a changing environment.

Managing Abiotic Stresses

At the Lubbock laboratory, plant physiologist Paxton Payton and postdoctoral 

research associate Rao Kottapalli are 

examining molecular mechanisms involved in peanut response to abiotic stress. 

Abiotic stress is the negative effect that 

nonliving factors, such as drought and 

heat, have on living organisms.

The researchers recently conducted 

groundbreaking work aimed at linking 

responses at the molecular level to the 

physiology and yields in peanut plants. 

They examined the proteins, particularly 

their expression, that control drought 

stress in peanut.

To examine diverse peanut germplasm 

more efficiently, Payton and Kottapalli 

performed greenhouse and molecular 

screening of 70 genotypes from the 

U.S. peanut mini-core collection and 7 

additional cultivars representing varieties 

commonly grown in the southern United 

States and semiarid regions in Asia. The 

mini-core collection—developed by 

ARS plant breeder Corley Holbrook in 

Tifton, Georgia—consists of 112 peanut 

accessions that represent most of the 

variation present in the larger collection 

of peanut germplasm.

Field screening of the 

accessions was performed 

by New Mexico State 

University scientist 

Naveen Puppala and a 

team of Texas AgriLife 

Research and Texas 

Tech University scientists led by Mark Burow. 

Photosynthetic measurements 

of the field-grown plants by Payton 

and Kottapalli helped narrow down the 

group to two accessions that are highly 

tolerant to heat and drought and two that 

are highly susceptible.

This follows previous work by the 

AgriLife and Texas Tech scientists 

and ARS scientists John Burke 

and Gloria Burow, who 

demonstrated heat and 

drought tolerance in a 

smaller set of peanut 

germplasm. They are 

now examining the inheritance of abiotic stress 

tolerance and hope to develop molecular markers that 

can be useful in breeding.

“Identifying drought responses in the mini-core 

collection can help us determine potential genetic 

components involved in 

abiotic stress tolerance,” 

says Payton. “Our study 

identifies potential targets 

for breeding and genetic 

engineering of abiotic stress 

tolerance in peanut crop plants.”

Perhaps most importantly, the phenotypes Payton and Kottapalli identified in 

the screening process were confirmed by 

field trials under stress-inducing conditions. Puppala and Burow are using the 

results of this and other screening 

experiments to make crosses 

to improve abiotic stress 

tolerance in peanut.

Payton and the researchers are also testing peanut’s response to 

other abiotic stresses. In 

recent tests, they found 

that the most heat-tolerant 

accessions were also the most 

drought tolerant. They also plan 

P

Preparing Peanuts for the Future

New Cultivars and Farming Strategies

Above: Drought-tolerant peanut yield from full irrigation (top) and deficit irrigation 

(bottom). Even with less water, drought-tolerant peanuts still yielded fairly well. 

Below: Drought-sensitive peanut yield from full irrigation (left) and deficit irrigation (right). 

With less water, the sensitive peanuts yielded about 90 percent less. 

PAXTON PAYTON (D1561-1) PAXTON PAYTON (D1562-1)

PAXTON PAYTON (D1560-1)

PAXTON PAYTON (D1559-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 33

to build on previous salt-stress work by 

AgriLife and Texas Tech scientists and 

conduct low-temperature screenings and 

tests in the coming year.

Developing New Farming Techniques

NPRL agronomist Wilson Faircloth and 

plant stress physiologist Diane Rowland 

(formerly with NPRL and now with Texas 

AgriLife Research) conducted field trials 

for 5 years in west Texas to determine 

the effects of deficit irrigation and, more 

recently, conservation tillage on peanut 

performance.

“Under deficit-irrigation management 

early in the season, plants appeared 

to reach maturity sooner than under 

late-season or other water deficits, and 

they maintained their yields,” says Faircloth. “Exposure to induced early-season 

drought may acclimate the crop to the 

drought stress that commonly occurs during late-season growth.”

It is also during this latter part of the 

growing season that growers typically 

experience water deficits due to reduced 

pumping capacity, further increasing the 

risk of yield loss.

“We wanted to find out whether conservation tillage with a cover crop could be 

used as an additional drought-mitigation 

tool,” says Faircloth. “To do this, we did 

a field study to compare traditional, highintensity tillage to conservation tillage 

with a rye cover crop.”

To be sure the research would hold up 

under grower conditions, the scientists 

tested it in one half of a center-pivot irrigation system located in Lubbock, Texas. 

They subdivided it into six half-acre 

sections and applied varying amounts of 

water to peanut and cotton planted in either conservation or conventional tillage.

“We used varying amounts of water 

to simulate a range of conditions—from 

normal season-long irrigation to earlyseason drought to late-season drought,” 

says Faircloth. Irrigation treatments were 

done in the traditional manner (meeting 

100 percent of the water need) and to 

simulate early-season drought (50 percent 

of the full amount for the first 45 days after 

crop emergence) and late-season drought 

(50 percent of the full amount for the 

45 days before harvest). Soil conditions 

and plant physiological responses were 

intensively monitored in the test areas. 

These included soil water content, plant 

photosynthetic rates, metabolic fitness, 

soil and canopy temperatures, rooting 

patterns, and tissue collections for genomic 

expression.

“Conservation tillage in the form of 

strip tillage was successfully demonstrated in this series of field tests, a first 

for peanut in this region,” says Faircloth. 

Additionally, under deficit irrigation, strip 

tillage increased yield when compared to 

conventional tillage. “This yield increase 

was attributed to increased water-holding 

capacity of the soil and changes in peanut 

rooting patterns. The combination of 

conservation tillage and deficit irrigation 

promotes conservation of water during 

the early season, and if implemented 

over a large geographic area such as the 

Southern High Plains, it has potential 

to significantly affect late-season water 

issues by reducing the amount of water 

needed for peanut irrigation.”

With more research, ARS will be able to 

help peanut farmers prepare for changes in 

the environment, which will help keep this 

delicious and nutritious legume available 

for generations to come.—By Stephanie 

Yao and Sharon Durham, ARS.

This research is part of Agricultural 

System Competitiveness and Sustainability 

(#216), Plant Biological and Molecular 

Processes (#302), and Quality and 

Utilization of Agricultural Products 

(#306), three ARS national programs 

described at www.nps.ars.usda.gov.

To reach scientists mentioned in this 

article, contact Stephanie Yao, USDA-ARS 

Information Staff, 5601 Sunnyside Ave., 

Beltsville, MD 20705-5129; (301) 504-

1619, stephanie.yao@ars.usda.gov. X

ARS physiologist John 

Burke and postdoctoral 

researcher Rao 

Kottapalli perform a 

chlorophyll fluorescence 

assay on peanut leaf 

samples from irrigated 

and drought-stressed 

plants. This assay is one 

of several that are used 

to screen germplasm 

for variability in 

abiotic stress tolerance. 

The monitor in the 

background shows 

an image of a peanut 

DNA microarray that 

is used to identify 

genes involved in 

stress response and to 

compare contrasting 

germplasm.

 STEPHEN AUSMUS (D1557-3)
34 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

field with bar codes, and their growth 

rates and other characteristics are carefully measured.

The project team includes Ed Buckler, 

a plant geneticist at the ARS Robert W. 

Holley Center for Agriculture and Health 

in Ithaca; plant geneticist Jim Holland 

in the ARS Plant Science Research Unit 

in Raleigh; plant geneticists Michael 

McMullen and Sherry Flint-Garcia in 

the ARS Plant Genetics Research Unit 

in Columbia; and Stephen Kresovich, a 

former Cornell University plant geneticist 

who is now vice president for research 

and graduate education at the University 

of South Carolina.

The NAM strategy consists of compiling two data sets—detailed genomesequencing data from the parent plants and 

a broader glimpse of the genetic details in 

the larger population—that can be crossreferenced to provide detailed genetic 

descriptions of all 5,000 lines. “If you 

want to look at the diversity of maize, with 

the 25 lines we chose as parents, this is as 

good as it gets,” says Buckler, a cofounder 

of the project.

Buckler, Holland, McMullen, FlintGarcia and others are using the NAM lines 

to search for quantitative trait loci (QTLs) 

and other signposts along the corn genome 

that can be linked to desirable qualities 

and traits. QTLs are stretches of DNA 

that might encode different combinations 

of traits.

The collection of NAM lines has proved 

invaluable not only to ARS scientists, but 

also to researchers at a dozen universities 

and a number of seed companies that use 

the lines to study a range of traits, including drought tolerance, disease resistance, 

and dozens of features related to nutritional quality and biofuel development. 

The work is addressing both practical and 

basic scientific questions, such as whether 

a few genes produce major effects or many 

genes produce minor effects, or whether 

some combination of both occurs. “It’s one 

of the first systematic ways to organize 

and map the genetic diversity of maize 

from around the world,” Buckler says.

Opening Up a New World of Maize 

Maize, or corn, is the most diverse crop 

species known. On average, two maize 

lines can be as genetically different as a 

human is from a chimpanzee, and such 

diversity can make sorting out the genetic 

basis of key traits particularly challenging. But a specially designed collection 

of maize lines is so large, diverse, and 

well-characterized that it has become a 

powerful and widely used genetic tool 

for researchers around the world who 

search for genes to enhance the crop’s 

desirable traits.

This collection of maize lines, called the 

“Nested Association Mapping” (NAM) 

population, has been developed by Agricultural Research Service scientists over 

the past several years by crossing a commonly studied corn variety (B73) with 25 

diverse lines and repeatedly self-fertilizing 

the offspring to create 5,000 inbred lines, 

each with a unique combination of the 

parental lines’ genetic traits. The resulting 

plants, grown at ARS sites near Ithaca, 

New York; Raleigh, North Carolina; and 

Columbia, Missouri, are tagged in the 

Steve Pigozzo, a North Carolina State University research assistant, pollinates a corn plant. 

JIM HOLLAND (D1928-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 35

Taking a Deeper Look at Photoperiod 

Sensitivity

Having developed the NAM population, Holland, Buckler, and their colleagues are now taking a closer look at 

some of the genes that control flowering 

time and a related characteristic known as 

“photoperiod sensitivity,” or sensitivity to 

day length.

The origins of maize can be traced 

to tropical Latin America. There, maize 

plants flower as the days grow shorter. 

When maize was carried from the tropical regions to temperate regions of the 

Americas, it had to adapt to the longer 

day lengths found during the summer in 

the temperate regions. Today, this adaptation is a major genetic difference between 

tropical and temperate maize.

“Tropical maize possesses genetic 

diversity that could be used to improve 

maize in temperate regions, such as the 

United States,” explains Holland. “But 

because tropical maize flowers very late 

when grown under long day lengths, 

undesirable traits such as poor yield can 

mask other favorable traits such as disease 

resistance. Our goal is to better understand 

the mechanisms behind photoperiod 

sensitivity so we can access the genetic 

diversity of tropical maize more easily.”

Buckler also says that understanding 

flowering time in corn would help in 

understanding it in other plant species. 

For example, if researchers want to move 

genetic material around within a plant’s 

genome to improve another trait, they 

need to know where flowering is controlled in the genome. “We don’t want to 

move a gene variant for disease resistance 

and inadvertently affect flowering time,” 

Buckler says.

In findings published last year in 

Science, the team reported that the large 

differences in flowering time among 

different lines of maize are caused by the 

cumulative effects of up to 56 QTLs, but 

that overall, each QTL has a relatively 

small effect.

“For an outcrossing species like maize, 

there are generally lots of genes with little 

Maize has tremendous genetic diversity. The nested association mapping (NAM) population is 

beginning to tap into some of this diversity to help improve corn.

Geneticist Sherry Flint-Garcia collects corn leaf tissue for DNA genotyping while Michael McMullen, 

also a geneticist, records field observations with a hand-held field computer.

KEITH WELLER (K7743-13)

 PEGGY GREB (D1919-1)

 Traits
36 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

effects. But if you line up these little effects together, you can do some very big 

things,” Buckler says.

Tropical-Temperate Crosses

In a separate project, Holland’s team 

crossed two tropical, photosensitive maize 

lines with two temperate maize lines. The 

tropical lines—one from Mexico, the other 

from Thailand—were chosen because they 

flower very late under the long day lengths 

of the U.S. Corn Belt. Including them in 

the study also helped Holland compare 

photoperiod response in tropical maize 

from different regions. The temperate lines 

represented the two main breeding pools 

found in the United States.

Through genetic mapping, the team 

sufficiently narrowed the maize genome 

to pinpoint four QTLs that are associated with photoperiod sensitivity. These 

QTLs—named “ZmPR1–4” by the researchers—represent 2 percent of the 

genetic map.

To genetically characterize their lines, 

Holland’s team used molecular markers 

originally developed by Buckler and 

McMullen for the NAM population. 

Although Holland’s lines were developed 

independently of the NAM population, 

they are now being integrated as an 

extension of the NAM population, because 

both populations were mapped using the 

same molecular markers.

“We also compared the QTLs responsible for photoperiod sensitivity with 

similar ones found in model plant species, 

such as Arabidopsis and rice,” says Holland. “We found related genes in maize 

and the model species—but not in the 

same important genomic regions. Some 

of the known photoperiod regulators in 

Arabidopsis and rice do not appear to be 

major photoperiod regulators in maize.”

Holland is currently confirming that 

the QTLs found in the tropical-temperate 

crosses are also important in the NAM 

population. “If we can focus on a few 

genome regions to select for genes that 

permit earlier flowering under long day 

lengths, the offspring will be better adapted to the long day lengths of temperate 

regions. Breeders can then focus on incorporating desired traits, such as increased 

yield and disease resistance, into U.S. 

maize varieties.”

Analyzing Recombination Effects

In Columbia, McMullen and collaborators genotyped 4,699 lines of the NAM 

population and were able to analyze 

136,000 “recombination events,” areas 

where the parental genes recombined. McMullen is a co-principal investigator of the 

project and leads genetic map construction 

of the NAM population—conducting gene 

sequencing, population development, 

genetic assays, and measuring plant traits 

in the field.

McMullen’s genetic mapping work has 

revealed enormous differences among 

families of corn plants with regard to recombination rates, which are the frequencies of physical exchanges of chromosomal portions from the different parents 

of a cross. They found that recombination 

rates are lower in the center of the chromosomes than in the chromosome ends. 

“This limits the possibilities for selecting a superior line. To be able to generate 

the best combinations of beneficial genes 

in a plant, you need strong recombination rates,” says McMullen. “And that’s a 

problem over much of the corn genome.” 

The findings, also published in Science

in 2009, highlight a challenge for the 

scientists: How to improve recombination 

rates in the central regions of the maize 

chromosomes.

Also in Columbia, Flint-Garcia is using 

NAM to understand the genetic control of 

kernel composition traits, such as starch, 

protein, and oil. She specializes in plant 

breeding, and her results could be used to 

genetically custom design corn kernels to 

fit the various oil-, starch-, and proteincontent needs of farmers and end users. 

“When designing maize for ethanol 

production, high starch is preferred,” says 

Flint-Garcia. “Poultry farmers prefer their 

maize feed to have high oil content.”—By 

Dennis O’Brien and Stephanie Yao, ARS, 

and Alfredo Flores, formerly with ARS.

The research is part of Plant Genetic 

Resources, Genomics, and Genetic Improvement, an ARS national program 

(#301) described at www.nps.ars.usda.gov.

To reach scientists featured in this article, contact Dennis O’Brien, USDA-ARS 

Information Staff, 5601 Sunnyside Ave., 

Beltsville, MD 20705-5129; (301) 504-

1624, dennis.obrien@ars.usda.gov.*

Michael McMullen records plant height with a 

hand-held field computer. 

Sherry Flint-Garcia examines and shells seed of 

the NAM inbred line founders. 

PEGGY GREB (D1918-3)

PEGGY GREB (D1921-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 37

ARS plant geneticist Peter Balint-Kurti (right) and postdoctoral researcher Adisu Negeri examine 

mutant corn plants for hypersensitive response lesions.

Two leaves from sibling plants. The plant on 

the left has the Rp1-D21 gene, which causes 

hypersensitive response (the mottled yellow 

appearance). The plant on the right doesn’t have 

this gene. 

PETER BALINT-KURTI (D1933-1) 

Do you believe in MAGIC? Agricultural 

Research Service plant geneticist Peter 

Balint-Kurti and colleagues at Purdue 

University do, especially when it comes 

to testing gene function in maize plants. 

But these scientists aren’t using card tricks 

or pulling rabbits out of hats. For them, 

MAGIC is an acronym that stands for 

“mutant-assisted gene identification and 

characterization.”

“MAGIC is a gene-centered approach 

that uses mutant genes or other genetic 

variants controlling a trait of interest as 

‘reporters’ to identify novel genes and 

variants for that trait,” explains BalintKurti, who is in the ARS Plant Science 

Research Unit in Raleigh, North Carolina. 

He teamed up with Guri Johal and Cliff 

Weil at Purdue to create MAGIC.

MAGIC offers researchers a new 

way of sifting through the large amount 

of natural genetic variation present in 

most plant species to identify and map 

versions of genes important for the control 

of specific agriculturally useful traits. 

MAGIC starts out with a clearly defined 

mutation affecting a trait of interest and 

then identifies other genomic regions that 

affect the same trait. By using a mutation, 

the trait in question can be exaggerated, 

making it easier to spot other genes 

affecting the trait that would not otherwise 

be readily detectable. The process involves 

crossing the mutant gene into plants with 

different genetic backgrounds and then 

evaluating the offspring for the strength 

of the mutant phenotype.

Balint-Kurti and colleagues demonstrated MAGIC’s usefulness when examining “hypersensitive response” in 

maize. Hypersensitive response is a 

defense mechanism used by all plants in 

which one or a few cells surrounding the 

site of pathogen attack essentially commit suicide to prevent further spread of 

the pathogen.

In a study published in Genetics, the 

researchers reported on mutant gene 

Rp1-D21, a partially dominant diseaseresistance gene that causes hypersensitiveresponse lesions to form spontaneously all 

over the plant—whether the pathogen is 

present or not. They found that the gene’s 

phenotype is profoundly affected by genetic background. The scientists crossed a 

plant containing Rp1-D21 with offspring 

of B73 and Mo17, two popular maize 

inbred lines. B73 partially suppresses the 

Rp1-D21 phenotype, and Mo17 partially 

enhances it. With this approach, the scientists identified a genomic location involved in the pathway controlling the start 

or local spread of hypersensitive response.

“By using the MAGIC technique, 

breeders can effectively screen the vast 

amount of genetic diversity present in 

maize—and in other plant species—for 

lines and genomic locations that have 

genes useful for controlling important 

plant traits, such as drought tolerance, 

sugar accumulation, and aluminum tolerance,” says Balint-Kurti. “In the present 

study, we are identifying variation controlling the plant defense response, which has 

been essentially invisible to us until now. 

This brings us one step closer to producing 

disease-tolerant cultivars.”

More hypersensitive-response studies are under way. Funded by the National Science Foundation, the scientists 

are now using MAGIC to screen the 

5,000-line Nested Association Mapping 

population—recently established by ARS 

scientists—for other genomic regions 

responsible for hypersensitive response. 

(See story on page 4 of this issue.)—By 

Stephanie Yao, ARS.

This research is part of Plant Genetic Resources, Genomics, and Genetic Improvement, an ARS national program (#301) 

described at www.nps.ars.usda.gov.

Peter Balint-Kurti is in the USDA-ARS 

Plant Science Research Unit, North Carolina State University, Gardner Hall, Room 

3418, Box 7616, Raleigh, NC 27695; 

(919) 515-3516, peter.balint-kurti@ars.

usda.gov.*

Want To Know What a Gene Does?

Use a Little MAGIC

 JOE BUNDY (D1934-1)
38 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Aspergillus flavus and A. parasiticus are 

naturally occurring soil fungi that are 

capable of invading food and feed crops 

and contaminating them with aflatoxin. 

Aflatoxin is a human carcinogen produced 

by the fungi and is also toxic to pets, livestock, and wildlife.

In addition to the safety hazard posed by 

aflatoxin contamination, the fungi place a 

significant economic burden on food and 

feed industries to ensure that contaminated 

products are prevented from reaching the 

food and feed supply.

Agricultural Research Service (ARS)

researchers in Georgia, Mississippi, 

and Louisiana are looking at different 

approaches for control of aflatoxin

contamination: One is “competitive 

exclusion”—using benign strains to 

impede colonization by harmful strains—

and the other is developing corn germplasm 

that resists buildup of aflatoxin.

Who’ll Win This Competition?

Recently retired microbiologist Joe 

Dorner at the National Peanut Research 

Laboratory in Dawson, Georgia, helped 

develop Afla-Guard, a biological control 

for A. flavus and A. parasiticus in peanuts.

Afla-Guard is composed of hulled 

barley coated with spores of a nontoxic 

strain of A. flavus. The nontoxic Aspergillus fungi successfully compete against 

the toxic species for the limited space and 

nutrients each needs to grow and thrive. In 

peanuts, Afla-Guard reduced aflatoxin by 

an average of 85 percent in farmers’ stock 

peanuts and up to 97 percent in shelled, 

edible-grade peanuts.

In light of this success, Dorner and other 

ARS scientists conducted a 2-year study 

of Afla-Guard in corn. They again found 

that it was effective in reducing aflatoxin 

levels—showing an overall reduction of 

85 percent, when compared to the levels 

found in control fields. 

Afla-Guard was applied to the corn crop 

in different ways: to soil when corn was 

less than a meter tall, in plant whorls prior 

to tassel formation, and as multiple sprays 

during silking.

“Afla-Guard has shown that it has a 

place in reducing aflatoxin in corn crops,” 

says Dorner. “After extensive study and 

research trials in Texas, Afla-Guard was 

registered by the U.S. Environmental Protection Agency (EPA) for use on corn, and 

that began with the 2009 crop.”

Neutralizing Mycotoxin

ARS scientists in Stoneville, Mississippi, are also using competitive exclusion 

to manage aflatoxin in corn. Their studies 

use a benign Aspergillus strain dubbed 

“K49” to outcompete the harmful fungi. In 

4 years of field trials, K49 applications to 

corn reduced aflatoxin by 60 to 94 percent.

To understand how K49 colonizes corn 

kernels, ARS plant pathologist Hamed 

Abbas used the pin-bar inoculation technique of applying the treatment. In this 

method, small finishing nails embedded in 

a wooden dowel are dipped in a K49 spore 

suspension and then used to penetrate corn 

husks in order to inoculate the kernels 

inside with the beneficial strain. 

“This benign Aspergillus culture reduces both the toxigenic species and the 

mycotoxins they produce, which is very 

exciting,” says Abbas, who is in ARS’s 

Crop Genetics Research Unit in Stoneville. A cooperative research and development agreement was established this year 

with industrial partners to develop the 

technology, and large-scale, multi-location 

field trials are in progress, he says. “We 

are developing novel formulations of K49 

and Afla-Guard to make foliar and aerial 

application feasible in the future.”

Other early research on competitive 

exclusion in cotton was done by ARS 

plant pathologist Peter Cotty, formerly in 

the ARS Food and Feed Safety Research 

Unit in New Orleans and now at the 

unit’s Tucson, Arizona, worksite. In 1996, 

ARS was awarded EPA approval to test 

one Aspergillus formulation, named 

“AF36,” in commercial cotton fields in 

Arizona. Successful testing paved the 

way for additional approvals and uses. 

EPA registration for use of AF36 on corn 

is pending.

Corn Germplasm Lines Resist 

Aflatoxin

“The presence of aflatoxin in corn grain 

greatly reduces its value and marketability,” says ARS geneticist Paul Williams, 

who has worked on identifying and developing corn germplasm lines with genetic 

resistance to A. flavus infection and the 

subsequent accumulation of aflatoxin.

Corn, in particular, has been hit hard by 

aflatoxin, with annual losses to the corn 

industry estimated at $192 million.

Williams, who is in the ARS Corn 

Host Plant Resistance Research Unit 

(CHPRRU) at Mississippi State, leads a 

multidisciplinary research team of five 

ARS scientists located at Mississippi State 

University and works with other university 

and ARS collaborators from several states.

Williams and his scientific team have 

developed and released germplasm lines 

that exhibit the highest known levels of 

resistance to A. flavus. In field trials conducted in Mississippi in 2008 and 2009, 

mean aflatoxin accumulation was about 95 

percent lower in the hybrids produced by 

crossing the ARS-developed germplasm 

lines than in a group of commercial hybrids adapted to Mississippi.

In the 2008 field trials, germplasm lines 

Mp715 and Mp717 exhibited the highest 

levels of resistance to aflatoxin contamination. In 2009 the recently developed 

germplasm line Mp04:097 performed well 

in the trials: Hybrids produced by crossing Mp04:097 with other resistant lines 

exhibited the lowest levels of aflatoxin 

accumulation.

Williams, geneticist Marilyn Warburton, and plant pathologist Gary Windham 

are also mapping quantitative trait loci 

(QTLs) associated with resistance to aflatoxin accumulation in crosses between 

resistant lines (Mp715 and Mp717) and 

susceptible lines with good agronomic 

qualities. Their goal is to identify linked 

markers that can be used in markerassisted breeding. Geneticist Matthew 

Krakowsky, in the ARS Plant Science 

Research Unit, Raleigh, North Carolina, 

has cooperated in these investigations.

Protecting Corn Crops from Aflatoxin
39

ARS researchers are working on different 

approaches to the problem of toxic Aspergillus fungi.

In Starkville, Mississippi, geneticist Paul 

Williams places bags over the tassels of 

corn plants with the desired molecular 

markers to collect pollen. 

STEPHEN AUSMUS (D1903-6) 

At Starkville, molecular geneticist Marilyn 

Warburton harvests leaf matter for DNA 

genotyping. The goal is to identify plants 

with markers for resistance to Aspergillus 

flavus and aflatoxin accumulation.

STEPHEN AUSMUS (D1901-11)

In Stoneville, Mississippi, plant pathologist 

Hamed Abbas uses the pin-bar inoculation 

technique to evaluate the colonization of 

corn by the biological control agent K49. 

STEPHEN AUSMUS (D1897-23)

To determine the resistance of corn lines 

to aflatoxin accumulation, plant pathologist 

Gary Windham injects Aspergillus flavus 

spores into corn ears grown in research 

plots at Starkville.

 STEPHEN AUSMUS (D1904-11)

Williams says, “Aflatoxin accumulation 

is highly sensitive to environmental variations, and resistance is a highly quantitative trait, meaning that it’s controlled by 

multiple genes. This makes breeding for 

resistance a challenge. We believe that 

molecular markers could be the key to the 

production of corn hybrids with resistance 

to aflatoxin accumulation.”

The research team also found that the 

Mp715 and Mp717 lines are resistant not 

only to aflatoxin accumulation, but also 

to fumonisin accumulation. Fumonisin, 

like aflatoxin, is a mycotoxin—a toxic 

metabolite—and is produced by F. verticillioides. The toxin causes neurologic 

abnormalities in horses—such as weakness of the face and pharyngeal muscles, 

facial desensitization, and a tendency to 

lean to one side—after they’ve consumed 

infected corn.

“These lines should be useful in developing corn lines and hybrids with 

resistance to both fumonisin and aflatoxin 

accumulation in grain,” says Williams. 

The lines have been widely requested 

and used in plant breeding programs in 

state, federal, and international research 

institutions plus three major commercial 

seed corn companies and several smaller 

companies.

The CHPRRU scientists have also 

developed and released corn germplasm 

lines with resistance to fall armyworm and 

southwestern corn borer, thus reducing the 

devastating leaf feeding by the two pests. 

Williams, along with CHPRRU agronomist Paul Buckley, tested 20 single-cross 

corn hybrids in laboratory bioassays: 

Larvae of both fall armyworm and southwestern corn borer weighed significantly 

less when fed the ARS-developed corn 

leaf tissue than when fed the susceptible 

hybrids. The CHPRRU scientists have 

demonstrated that growing hybrids that 

sustain less damage from such ear-feeding 

insects as fall armyworm, southwestern 

corn borer, and corn earworm results in 

reduced aflatoxin contamination.

In related research, by comparing 

aflatoxin-susceptible with aflatoxinAgricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 39
40 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

resistant corn lines (some developed by 

Williams), ARS plant pathologist Robert 

Brown in New Orleans identified and 

characterized a number of proteins that 

may be important in imparting resistance 

to corn. (See “Hardy New Corn Lines Resist Toxic Fungi,” Agricultural Research,

Oct. 2009, p. 14.) In the collaboration with 

Warburton mentioned above, the genes 

for these proteins have been mapped to 

chromosomal regions containing QTLs 

previously linked to aflatoxin resistance 

in the corn genome. These specific resistance-associated proteins can serve as 

targets for the marker-assisted breeding 

being carried out in Mississippi.

Expanding our horizons in corn breeding, Brown, with financial support from 

the USDA Foreign Agricultural Service, 

the United States Agency for International Development, and the ARS Office 

of International Programs, established a 

collaborative breeding program with the 

International Institute of Tropical Agriculture in Ibadan, Nigeria, which recently 

released six aflatoxin-resistant corn lines. 

These lines, the product of up to 10 generations of selection and inbreeding, have 

In Stoneville, Mississippi, biologist Bobbie 

Johnson adds ammonium hydroxide to 

Aspergillus cultures to differentiate aflatoxinproducing strains (yellow and red) from 

nonproducers (off-white).

STEPHEN AUSMUS (D1896-6)

Marilyn Warburton and geneticist Paul Williams tag corn plants identified in the lab as having 

molecular markers associated with resistance to Aspergillus flavus and aflatoxin accumulation. 

These tagged plants will be crossed with other breeding lines to develop resistant corn hybrids. 

STEPHEN AUSMUS (D1902-5)

passed quarantine and are now available 

in the United States from the ARS North 

Central Regional Plant Introduction Station, Ames, Iowa.—By Sharon Durham

and Jan Suszkiw, ARS, and Alfredo 

Flores, formerly with ARS.

This research is part of Food Safety 

(#108), Plant Genetic Resources, Genomics, and Genetic Improvement (#301), 

Plant Diseases (#303), and Crop Production (#305), four ARS national programs 

described at www.nps.ars.usda.gov.

To reach scientists mentioned in this 

story, contact Sharon Durham, USDAARS Information Staff, 5601 Sunnyside 

Ave., Beltsville, MD 20705-5129; (301) 

504-1611, sharon.durham@ars.usda.

gov. *
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 41

Citrus plants are highly susceptible to a disease commonly called “HLB” 

(Huanglongbing), also known as “citrus 

greening disease.” Agricultural Research 

Service scientists in the Quality and Safety 

Assessment Research Unit in Athens, 

Georgia, and the Subtropical Plant Pathology Research Unit in Fort Pierce, Florida, 

joined forces to use a technology known 

as “Fourier transform infrared-attenuated 

total reflection” (FTIR-ATR) spectroscopy 

to identify citrus greening-infected plant 

leaves with 95-percent accuracy.

Citrus greening was discovered in 

Florida in 2005 and is rapidly spreading in 

the citrus-growing regions of the state. The 

disease is transmitted by the Asian psyllid, 

an insect found throughout Florida. Fruit 

from infected trees drops prematurely or 

fails to ripen.

A 2007-2008 survey conducted by the 

University of Florida, in collaboration with 

USDA’s National Agricultural Statistics 

Service and the Florida Department of 

Agriculture and Consumer Services, 

included 153,000 net acres of oranges 

and 17,676,000 orange trees. The survey 

revealed that growers—to prevent spread 

of disease—removed 847,208 infected 

trees during the survey period. Plants can 

be infected for up to several years before 

showing symptoms, and during this period 

the psyllid can transmit the disease agent 

to nearby plants.

Currently, the best method for detecting 

citrus greening-infected trees is a type 

of DNA testing called PCR (polymerase 

chain reaction), which is both costly and 

time consuming.

FTIR uses light to identify chemicals and 

reactions in a sample. This technology has 

the potential to detect the disease before 

visible symptoms occur and is cheaper 

and faster. The mid-infrared region of the 

electromagnetic spectrum reveals dramatic 

changes that occur in leaves of infected 

trees compared to leaves from noninfected 

trees. The results from this technique’s 

application were published in the journal 

Applied Spectroscopy in 2010.

To create the new technology, experts 

from both labs were needed. “ARS is great 

in this respect because it has so many experts with which to collaborate,” says ARS 

researcher Gavin Poole in the Fort Pierce 

unit. “Research leader Tim Gottwald and I 

had an idea to use spectroscopic methods to 

identify citrus greening before symptoms 

develop in the field, and our colleagues in 

Georgia were able to use their expertise to 

help us attack this problem.”

The Athens team included chemist 

Samantha Hawkins, engineer Bosoon 

Park, physiologist William Windham, and 

research leader Kurt Lawrence. Hawkins 

used an FTIR spectrometer with an ATR 

crystal accessory to test for the presence 

of citrus greening.

“We used a leaf removed from the 

citrus tree, dried it out in a microwave, 

and ground it into a powder—a simple 

protocol developed by Windham,” says 

Hawkins. A very small sample—just 

0.1 milligrams—of the leaf powder was 

placed on top of an ATR plate. The system 

clearly discriminated HLB-infected leaves 

from healthy leaves. More work will be 

needed to discriminate HLB from other 

citrus diseases.

“This is a great method because the 

sample preparation is faster and easier 

than PCR, which is typically used to get a 

value of how much disease is in the leaves,” 

says Hawkins. “Growers currently send 

leaf samples out for PCR analysis that 

costs about $6 to $8 per sample and takes 

several days. The FTIR technique is done 

in seconds.”—By Sharon Durham, ARS.

This research is part of Plant Diseases, 

an ARS national program (#303) described 

at www.nps.ars.usda.gov.

Samantha Hawkins is in the USDA-ARS 

Quality and Safety Assessment Research 

Unit, 950 College Station Rd., Athens, 

GA 30605; (706) 546-3454, samantha.

hawkins@ars.usda.gov.

Gavin Poole is in the USDA-ARS Subtropical Plant Pathology Research Unit, 

2001 South Rock Rd., Fort Pierce, FL 

34945; (772) 462-5940, gavin.poole@

ars.usda.gov.*

Symptoms of HLB 

(Huanglongbing), 

also known as 

“citrus greening 

disease.”

TIM GOTTWALD (D2259-1)

Identifying Trees 

Infected With 

Citrus Greening
42 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

The Steinernema carpocapsae nematode is a little worm 

that can protect peach and other 

stone fruit trees by attacking 

devastating borer pests. Some 

nematodes are pests, but these 

are beneficial because they can 

act as biological controls of the 

borers and other insect pests.

Trouble is, this nematode is 

sensitive to the sun’s harmful 

ultraviolet rays and heat, both of 

which can cause desiccation—

the state of extreme dryness. In 

time this can cause death, so the 

nematodes could benefit from 

some sort of protection when 

exposed to these elements.

Agricultural Research Service scientists in Byron, Georgia, are trying a novel approach 

to help the tiny worms. They’re 

testing the same type of “fire 

gel” that has been used to help 

prevent the spread of fire to 

residential and commercial 

structures to see whether the 

gel, after it is sprayed onto fruit 

trees, can help nematodes avoid 

desiccation.

The gel creates a barrier between the fire and the structure 

it’s protecting, preventing the spread of 

fire. This barrier property could also serve 

as a moisture “blanket” for nematodes, allowing them to attack pests above ground 

without being harmed by the sun.

There are two species of borers that 

attack peaches—lesser peachtree borers, 

which attack the aboveground portions of 

the peach tree, and peachtree borers (also 

known as greater peachtree borers), which 

attack the roots of the tree. In laboratory 

settings, S. carpocapsae nematodes proved 

effective in killing both borer species.

The nematodes are efficient 

at controlling the undergrounddwelling peachtree borer but 

lose their effectiveness above 

ground. That’s because the 

nematodes’ chances of survival 

are far greater below ground—

where the soil’s moisture helps 

them stave off drying—than 

above ground, where they’re 

exposed to sun and heat.

According to entomologist David Shapiro-Ilan, with 

ARS’s Southeastern Fruit and 

Tree Nut Research Laboratory 

in Byron, “If fire gels can protect a house, they may be able 

to protect nematodes for a few 

days so that they can kill the 

lesser peachtree borer.”

And he’s shown that the gel 

does just that. Shapiro-Ilan, 

along with fellow Byron entomologist Ted Cottrell, tested 

different formulations aimed 

at protecting the nematodes 

during aboveground application, including the fire gel.

After 2 years of testing, a 

nontoxic, environmentally 

friendly brand of fire gel (Barricade) was the most effective 

treatment. The best part was that the gelnematode combination left only 30 percent 

of the lesser peachtree borers alive in 2008 

(from 100 percent initial survival), and 

none survived in 2009.

The scientists believe the sprayable gel 

could be used to protect other beneficial 

“Fire Gel” Protects Beneficial 

Nematodes From Sun

Peaches grown at the USDA-ARS Southeastern Fruit and Tree Nut 

Research Laboratory.

PEGGY GREB (D2080-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 43

The scientific team plans to test the 

fire gel on grower orchards. Horton, who 

also serves as an extension specialist, will 

be instrumental in finding these grower 

cooperators. Horton is developing an 

instructional video offering farmers tips 

on how best to apply the gel. Mizell will 

conduct field trials in Quincy, Florida, to 

determine the best time of year to apply 

the gel and to see whether Shapiro-Ilan’s 

technology is applicable in that region.

Shapiro-Ilan is also working with ARS 

collaborators Bob Behle and Chris Dunlap 

in Peoria, Illinois, as well as Lerry Lacey in 

Wapato, Washington. Behle, an entomologist, and Dunlap, a chemist, specialize in 

formulation of microbial agents and have 

provided Shapiro-Ilan with some of the 

ingredients needed for his field trials.

Lacey, an entomologist, has developed 

a foam formulation that consists of wood 

species besides S. carpocapsae. The gel 

might be used in combination with other 

beneficial nematodes to control a wide 

range of pests in trees or other crops above 

ground.

Shapiro-Ilan and Cottrell received funding from a U.S. Department of Agriculture 

Pest Management Alternatives Program 

and collaborated with entomologists Dan 

Horton at the University of Georgia and 

Russ Mizell at the University of Florida.

Entomologist David Shapiro-Ilan (left) sprays 

a gel formulation onto a peach tree limb 

while technician Wanda Evans prepares the 

nematode application. The gel is being used 

to protect beneficial nematodes from damage 

due to extreme drying and UV radiation. With 

the protective formulation, the nematodes go 

to work killing harmful insect pests, such as the 

lesser peachtree borer.

PEGGY GREB (D2077-1)

Fire-gel sprayed onto peach tree limbs.

PEGGY GREB (D2078-2)
44 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

fiber, wood flour, and starch. This formulation forms a protective crust, whereas 

the gel is sticky.

Shapiro-Ilan has tested the two formulations—gel and foam—and found 

that the gel worked best for borers in 

the southeast, possibly due to the hot, 

dry climate. Lacey found that the foam 

worked better in the wet, cool northwest, 

protecting nematodes that attack the 

codling moth, a destructive pest of apples 

and pears. Shapiro-Ilan and Lacey will 

continue to test the formulations under a 

variety of conditions.

The scientific team is researching how 

to further optimize application rates and 

timing and to perform large farm-scale 

tests using air-blast sprayers to apply 

the fire gel. The scientists will also test 

air handgun sprayers, which efficiently 

disperse the fire gel in a uniform spray 

pattern. Additional laboratory tests are 

being conducted in search of superior 

nematode strains.

“We’re going to test how much and 

how often we’d like to disperse the fire gel 

through these means,” said Shapiro-Ilan, 

who plans to work with small and organic 

growers first and continue with largescale growers in the next few years. 

“We’d like to make this process as 

efficient and economical as possible 

so we can get the most bang for our 

buck. Growers are savvy enough 

that if something makes economic sense, they’re going to do it.”—

By Alfredo Flores, formerly with ARS.

This research is part of Crop Protection and Quarantine, an ARS national 

program (#304) described at www.nps.

ars.usda.gov.

David I. Shapiro-Ilan and Ted Cottrell 

are at the USDA-ARS Southeastern Fruit 

and Tree Nut Research Laboratory, 21 

Dunbar Road, Byron, GA 31008; (478) 

956-6444 [Shapiro-Ilan], (478) 956-6448 

[Cottrell], david.shapiro@ars.usda.gov, 

ted.cottrell@ars.usda.gov.*

Entomologists Ted Cottrell (above left) 

and David Shapiro-Ilan observe beneficial 

nematodes (Steinernema carpocapsae) 

that are used to control the lesser 

peachtree borer. Shapiro-Ilan and Cottrell 

developed a sprayable gel as a novel 

method for protecting the nematodes 

from desiccation (extreme dryness) and 

UV radiation.

PEGGY GREB (D2082-1)

Inset: A lesser peachtree borer larva (Synanthedon 

pictipes) emerging from a wound it made in a peach tree. 

Right: A wound in a peach limb made by lesser 

peachtree borer (Synanthedon pictipes).

PEGGY GREB (D2081-1)

PEGGY GREB (D2079-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 45

If the next jar of pickles you reach for 

looks a little red—stop! From time to 

time pickled cucumber products can get a 

red coloration indicative of benign spoilage bacteria. Though this doesn’t happen 

often, it can still be an unpleasant experience. ARS scientists in the Food Science 

Research Unit (FSRU) in Raleigh, North 

Carolina, have found its cause, how to 

prevent it, and more.

According to ARS 

microbiologist Ilenys 

Pérez-Díaz and her colleagues, some species 

of Lactobacilli—foodrelated microorganisms—can cause the 

red coloring when combined with tartrazine, 

which is a yellow foodcoloring agent.

But Lactobacilli can 

be beneficial, too. During testing, the FSRU 

team noted that several Lactobacilli also 

modify azo dyes—dyes used in the textile industry that may be passed along to 

wastewater streams if untreated. This is the 

first report that food-related microorganisms can transform azo dyes.

Azo dyes impart vivid and warm colors 

such as red, orange, and yellow to fabric. 

Though many azo dyes are nontoxic, some 

have been found to be mutagenic. “Considerable effort has been made to identify 

microorganisms capable of degrading azo 

dyes in wastewater streams from the textile 

industry,” says Pérez-Díaz. “If food-grade 

Lactobacilli capable of degrading a range 

of azo dyes were identified, they might be 

organisms of choice for waste-treatment 

applications.”

This revelation spawned from research 

that began long ago.

Thirty years ago, ARS scientists fingered Lactobacillus casei as the cause of 

the red spoilage. Another outbreak some 

years later prompted further research, 

which identified another bacterium in the 

Lactobacillus genus —L. paracasei—as 

the culprit when FD&C yellow no. 5 (tartrazine) was added to the brine solution. 

Commercial dill pickle makers use either 

this dye or turmeric to impart a yellowish 

tint to the pickles’ brine.

Pérez-Díaz and her colleagues isolated 

Lactobacilli from spoiled jars of hamburger dill pickles and used those isolates 

to inoculate nonspoiled jars of hamburger 

dill pickles. “Jars that contained brines 

with tartrazine developed the red hue on 

the pickle skins; those that had turmeric 

or no added coloring did not,” she says. 

“We also found that pH level played a role 

in the development of red discoloration 

on pickle skin. A pH between 3.9 and 3.5 

supported bacterial growth, disappearance 

of tartrazine, formation of red-colored 

spoilage, and a drop in pH.” 

Seven treatments were tested in an 

Pickle Spoilage Culprit

May Give the Environment a Helping Hand

attempt to find a preventive measure for 

red-colored spoilage. Pérez-Díaz found 

that adding sodium benzoate prevented 

bacterial growth, disappearance of tartrazine, and development of red spoilage. 

According to Pérez-Díaz, this would be a 

practical method to prevent development 

of red-colored spoilage in hamburger dill 

pickles.—By Sharon Durham, ARS.

This research is part of Quality and 

Utilization of Agricultural Products, an 

ARS national program (#306) described 

at www.nps.ars.usda.gov.

Ilenys Pérez-Díaz is in the USDA-ARS 

Food Science Research Unit, 322 Schaub 

Hall, Box 7624, North Carolina State 

University, Raleigh, NC 27695-7624; 

(919) 513-0165, ilenys.perez-diaz@ars.

usda.gov.*

Inset: Microbiologist Ilenys Pérez-Díaz uses spectrophotometry to examine loss of yellow coloring 

in a sample of cucumber brine. Above: A preserved cucumber that has developed red-colored 

spoilage from Lactobacilli. 

PEGGY GREB (D1891-1)

PEGGY GREB (D1892-1)
46 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

When chewed on by hungry 

caterpillars, corn, cotton, 

and tobacco plants release 

chemical distress signals 

that marshal help from parasitic wasps. 

Similarly, lima beans attacked by spider 

mites attract predatory mites. 

Now, an Agricultural Research ServiceUniversity of Florida team has shown that 

some citrus trees also resort to signaling when their roots are attacked by the 

grublike larvae of Diaprepes abbreviatus,

the citrus root weevil. But instead of fastflying wasps or nimble-legged predatory 

mites, the rescuers are wormlike organisms 

called “nematodes,” which wriggle inside 

the grubs and feed on them internally, 

killing the citrus pests in 24 to 48 hours. 

“When weevil larvae feed on roots,” 

says ARS chemist Hans Alborn, “the roots 

release volatiles, including terpenes, that 

diffuse into the surrounding soil.” Nematodes in the soil track those chemical cues 

back to their source—namely, roots needing rescue from further harm. 

Potentially, the finding could yield new, 

improved ways of using the nematodes to 

Could Improve

Use of Nematode 

“First Responders”

biologically control D. 

abbreviatus. The species, 

which is native to the 

Caribbean region, was 

accidentally introduced 

into Florida in 1964. 

Today, it’s considered a 

major agricultural pest 

that causes $70 million 

annually in losses not 

only to citrus, but also 

to ornamental plants and 

other crops. 

The weevil also poses 

an aboveground threat 

to Florida’s citrus crop, 

valued at $993 million 

during the 2008-2009 

season. As an adult, the pest feeds on 

leaves, giving them a notched appearance. 

“Notching is one of the first things you 

see when entering an infested grove,” 

says Jared G. Ali, a University of Florida 

researcher collaborating with Alborn, who 

is in the ARS Chemistry Research Unit in 

Gainesville, Florida. 

Adult weevils can be controlled by 

spraying the tree canopy with foliar insecticides. Also effective, though far more timeconsuming and labor-intensive, is shaking 

the canopy and trapping the weevils that 

fall from trees or emerge from the soil. 

Synthetic pyrethroids are used to control the grubs. Some of these chemicals 

are meant to serve as a barrier to larvae 

that fall to the ground after hatching from 

eggs deposited in the canopy. Even then, 

“many larvae still make it into the soil,” 

notes Ali, who works in the laboratory of 

Lukasz Stelinksi, an assistant professor 

Citrus Chemical 

Call to Arms 

Found

peggy greb (d2053-1)

peggy greb (D2057-1)

peggy greb (D2051-1)

Above: University of Florida collaborator Jared 

Ali adds insect-killing nematodes to a six-arm 

olfactometer to test their attraction to different 

citrus rootstock cultivars attacked by Diaprepes 

root weevil larvae. The olfactometer is filled with 

sandy soil to simulate conditions below ground. 

ARS chemist Hans Alborn loads an autosampler 

with vials for gas chromatography and mass 

spectrometer analyses of root volatile collections.

A Diaprepes weevil feeds on a citrus leaf.
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 47

at the University of Florida’s 

Citrus Research and Education 

Center in Lake Alfred, Florida.

Once below ground, the 

grubs feed on the tree’s fibrous 

roots until ready to pupate, 

emerging as adults anywhere 

from 6 to 15 months later. 

Severe infestations weaken the 

tree and reduce overall fruit 

yield. Feeding also increases 

the likelihood of infection by 

Phytophthora fungi, which 

cause root rots that can speed 

the tree’s demise at great cost 

to growers. 

Biological Alternatives

Life below the citrus grove 

is not without its hazards, however. That’s because the grubs 

are a favorite food of some species of insect-killing, or “entomopathogenic,” nematodes 

such as Steinernema riobrave

and Heterorhabditis indica.

Both have been commercially 

formulated into biopesticide 

products that can be applied 

to grub-infested groves using existing 

herbicide applicator technology or other 

micro-sprinkler systems. 

After encountering a grub, and infecting 

it, the nematodes release symbiotic bacteria 

that render the pest’s tissues into a kind 

of slurry, which the nematodes then eat. 

Once the food is gone, the nematodes exit 

the carcass to start the cycle over again. 

The nematodes and their bacteria target a 

slew of insect hosts, but pose no danger 

to humans, pets, livestock, or wildlife. 

A variety of factors, including soil type 

and temperature, can affect the nematode’s 

performance as a biocontrol agent—with 

reductions in grub numbers at treated sites 

ranging from 0 to 90 percent. But until 

recently, little attention had been paid to 

the complex chemical tête-à-tête that occurs between citrus tree roots, grubs that 

feed on them, and the surrounding soil’s 

resident nematodes. 

When a plant chemically recruits a predator or parasite to dispatch of a herbivorous 

attacker—in this instance, citrus calling on 

nematodes to kill grubs—scientists call 

the phenomenon a “tritrophic interaction.” 

While aboveground tritrophic interactions are well documented, far less is known 

about underground ones. 

“We’re one of the first groups to look at 

these interactions from a citrus-chemical 

ecology perspective,” says Ali who coauthored a paper on the work with Stelinksi 

and Alborn in the March 2010 issue of the 

Journal of Chemical Ecology. “Our specific 

focus is gaining insight into what a citrus 

plant can do to protect itself,” Ali adds.

Catching the Action in Real-Time

To determine what signaling compounds 

citrus roots released when attacked by 

grubs, the scientists used a specialized glass 

chamber called a “root-zone 

olfactometer.” 

“With this system, you can 

see the weevils chewing on 

the roots and pull the volatiles 

off as they’re being released,” 

says Ali. “You can also tease 

out which direction the nematodes are going” and extract 

them for analysis, he adds.

In lab and greenhouse trials 

with small trees derived from 

the commercial rootstock 

“Swingle citrumelo,” roots 

damaged by captive grubs attracted up to three times more 

S. diaprepesi nematodes than 

roots that had been mechanically damaged or left intact. 

When root volatiles were 

collected and analyzed by gas 

chromatography-mass spectrometry, terpenes accounted 

for four of the six compounds 

that stood out. Interestingly, 

“the roots only released the 

volatiles when being fed on 

by larvae,” notes Alborn. 

The team’s research could 

one day lead to new varieties 

developed from rootstocks 

shown to be adept at recruiting 

nematodes. So far, they have 

tested the signaling capacities 

of 5 rootstocks and hope to screen as many 

as 20 more by the end of 2011. 

The researchers are also studying the 

volatiles’ effect on other denizens of the 

citrus root zone, including nematodes that 

parasitize plants. 

Within the next 2 years, the team hopes 

to recommend rootstock-nematode combinations that growers can use as part of 

an integrated approach to managing the 

weevil.—By Jan Suszkiw, ARS. 

This research is part of Crop Protection 

and Quarantine (#304) and Crop Production (#305), two ARS national programs 

described at www.nps.ars.usda.gov.

Hans Alborn is in the USDA-ARS Chemistry Research Unit, Center for Medical, 

Agricultural, and Veterinary Entomology, 

1600-1700 S.W. 23rd Dr., Gainesville, FL 

32608; (352) 374-5714, hans.alborn@ars.

usda.gov.*

A chamber used in an underground field test 

of nematode attractants. The chamber is filled 

with sand, a root weevil larva, and a filter paper 

impregnated with the attractant.

PEGGY GREB (D2055-1)

University of Florida assistant 

professor Lukasz Stelinski 

applies a nematode attractant 

to a nematode lure to be tested 

below ground in a citrus field.

PEGGY GREB (D2054-1)
48 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

As they search for soil treatments

to replace methyl bromide, Agricultural 

Research Service scientists in Fort Pierce, 

Florida, are using one technique that sounds 

as if it were borrowed from a family recipe 

—taking molasses and heating it up.

Farmers have been using methyl bromide since the 1930s, but these days it is 

subject to strict environmental controls 

because it depletes Earth’s ozone layer. As 

part of an international agreement, growers worldwide are being required to find 

a replacement, a tall order because methyl 

bromide eliminates a broad spectrum of 

pests, including weeds, nematodes, and 

plant pathogens. The mandate is particularly challenging in Florida, where sandy 

soils limit organic alternatives and the mild 

winters serve as a safe harbor for many of 

nature’s most pernicious pests. Nutsedge 

is a particular weed problem in Florida 

and is a major reason methyl bromide is 

still used there.

“We don’t usually see the cold winter 

temperatures that you have in other places, 

so pests aren’t killed off here by Mother 

Nature the way they might be elsewhere,” 

saysErin Rosskopf, a microbiologist at the 

U.S. Horticultural Research Laboratory in 

Fort Pierce.

For Florida growers, the stakes 

are enormous. Fresh-market tomatoes and bell peppers, both raised 

in Florida with methyl bromide, 

netted growers there a combined 

$889 million in 2008. Caladiums, 

an ornamental also produced 

largely with methyl bromide, are 

a $15 million crop in Florida.

In their search for alternatives, 

ARS researchers are studying two 

approaches: a biologically based 

cropping system that builds on 

success overseas, and two recently 

developed fumigants. Similar approaches have had some success elsewhere, 

but the question is whether they will be 

effective in Florida, with its unique soils, 

climate, and pest pressures. Preliminary 

results are promising, but the researchers 

still need to evaluate whether the biologically based treatments can sufficiently 

control nutsedge.

A Biological Alternative

At the Fort Pierce lab, Rosskopf, ecologist Nancy Kokalis-Burelle, and soil scientist David Butler are raising bell peppers 

followed by eggplant in a field to test a 

biological approach that uses a combination of composted broiler litter, molasses, 

and anaerobic soil disinfestation (ASD). 

Lab colleagues Gregory T. McCollum and 

Joseph Albano are evaluating fruit quality 

and soil nutrients.

In ASD, a carbon source—in this case 

molasses—is added to stimulate microbial 

activity, and the soil is covered with a 

clear plastic tarp. The topsoil is saturated 

with water and allowed to heat. The sundrenched tarp “cooks” the weed seeds in 

the soil, and the carbon and water increase 

microbial activity and create anaerobic 

conditions conducive to pest control.

In this study, before heating the soil, 

the researchers treated plots with different 

levels of organic amendments: with and 

without poultry litter; with and without 

molasses; and with 2 inches of water per 

acre, 4 inches per acre, or no water at all. 

The poultry litter increased soil moisture 

and added organic matter, and the molasses 

provided a readily available carbon source 

for soil microbes. The molasses they used 

is a waste product of the sugarcane processing industry. The researchers are also 

conducting studies to evaluate mustard 

meal, sorghum, and cowpeas as possible 

alternatives to molasses.

They planted peppers in the fall and 

eggplant in the spring for 2 years, using 

the type of raised-bed production system 

common in Florida. Before planting, the 

researchers introduced Phytophthora capsici to the fields, an oomycete that causes 

crown rot and root rot, so they could track 

control rates. They buried packets of it 6 

Investigating T

to Replacing M

In an anaerobic soil disinfestation trial for growing eggpla

nutrient analysis and plant pathogen population assessm

PEGGY GREB (D2132-1)

Technician Amanda 

Rinehart (foreground) 

and ecologist Nancy 

Kokalis-Burelle study 

eggplant roots for 

nematode damage 

and root health.
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 49

inches deep in the soil and retrieved them 

after 3 weeks of ASD to evaluate the effects. 

They also sampled the soil for nematodes, 

counted the number of nematodes extracted 

from crop roots, assessed weed populations 

and soil properties throughout the trials, 

and measured crop yields.

They found that at depths of 6 inches, 

the ASD treatments heated the soil temperature to about 113 ̊F, which was at 

or just below lethal levels for many soil 

pathogens. They also found that nematode 

populations were reduced when treated 

with molasses and poultry litter, that molasses and poultry litter controlled grass 

weeds just as well as methyl bromide did, 

and that the ASD treatments controlled P. 

capsici in the buried packets as well as 

methyl bromide did, regardless of how 

much water, poultry litter, or molasses 

was applied. 

“The nutsedge pressure at 

the test location wasn’t really 

adequate to show treatment 

differences, so we are still 

investigating that component,” Rosskopf says.

Evaluating New 

Commercial Products

Rosskopf and Kokalis-Burelle completed large-scale demonstration field 

trials comparing the effectiveness of two 

recently developed fumigants with methyl 

bromide at two Florida sites, one where 

they are raising delphiniums and the 

other caladiums. Both dimethyl disulfide, 

approved for experimental use under the 

trade name “Paladin,” and methyl iodide, 

being marketed as “Midas,” have shown 

promise at controlling weeds, nematodes, 

and plant diseases.

The researchers combined each treatment with chloropicrin, a pesticide that kills 

fungi and is often used in combination with 

methyl bromide. They applied each treatment to about a half-acre of delphiniums 

in a field in Hobe Sound and 2 acres of 

caladiums at another site in Zolfo Springs. 

They raised two varieties of delphiniums 

and four varieties of caladiums. 

In the caladium trials, where the pest 

pressure was much higher than in the 

delphinium trial location, their grower 

cooperator also applied a soil treatment 

often used on caladiums known as “Telone 

II” (1,3-dichloropropene). They measured 

weed density, weeding time required, and 

nematode and fungal populations in the 

soil. They also examined roots for disease 

and compared the sizes and numbers of 

flowers produced under each treatment.

Preliminary results show the alternative 

fumigants were just as effective as methyl 

bromide at suppressing grass weeds and 

at controlling nematodes, but that the effectiveness of Paladin was reduced when 

it was used year after year.

In the delphinium trial, there were no 

significant differences in weed density 

and total weeding time or in total flower 

yields. In the caladium trial, they found 

no significant differences among methyl 

bromide, Paladin, and Midas in terms of 

total weeds, “rogue” or off-variety plants 

produced, or in total hours of labor for 

weeding, but yields were dependent on 

the combination of fumigant and cultivar. 

“This interaction indicates that growers will have harder decisions to make, 

because their choice of cultivar is often 

market-driven. They may have to choose 

a fumigant that provides the greatest return 

for that specific cultivar, making it much 

more difficult than when they could use 

methyl bromide with everything they 

grew,” said Rosskopf.

The fumigant field trials are attracting 

widespread interest. A recent field day 

organized to explain the project at Zolfo 

Springs attracted dozens of cut-flower and 

caladium growers.—By Dennis O’Brien, 

ARS.

This research is part of Methyl Bromide 

Alternatives (#308), an ARS national program described at www.nps.ars.usda.gov.

To reach scientists mentioned in this 

article, contact Dennis O’Brien, USDAARS Information Staff, 5601 Sunnyside 

Ave., Beltsville, MD 20705-5129; (301) 

504-1624, dennis.obrien@ars.usda.gov.*

Two Pathways

Methyl Bromide

Bell peppers and a wide variety of other vegetables and fruits may 

benefit from anaerobic soil disinfestation, a potential alternative to 

methyl bromide fumigation for pest control.

ant, soil scientist David Butler collects a soil sample for 

ment.

david Butler (D2133-1)

PEGGY GREB (D2131-1)
50 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Microcracksin the shells 

of eggs pose 

a major food safety concern to consumers. 

Research has shown that cracked eggs are 

more likely to harbor bacteria, including 

foodborne pathogens. A new technology—

called the “modified-pressure imaging 

system”—combines negative pressure 

with imaging and can accurately detect 

almost 100 percent of cracked eggs.

The device, developed by Agricultural 

Research Service scientists in Athens, 

Georgia, was discussed in detail in “A 

Better Way To Spot Eggshell Cracks,” 

Agricultural Research, February 2009. It 

uses a negative-pressure chamber to essentially pull the eggshell outward very 

gently to clearly show any microcracks 

present in the shell. 

The next step was to see whether quality suffered after eggs were subjected to 

the device.

Food technologist Deana Jones, research leader Kurt Lawrence, engineer 

Seung-Chul Yoon, and hyperspectral image specialist Gerald Heitschmidt, in the 

Egg Safety and Quality Research Unit, 

conducted a study to determine whether 

exposure to the modified-pressure imaging system had any effect on egg quality 

during storage. 

“After 5 weeks of refrigerated storage, 

only a slight difference in the amount of 

water in the whole egg was noted between 

imaged and nonimaged eggs,” says Jones. 

“All other quality attributes were the same 

for imaged and nonimaged eggs.”

These other quality attributes include 

the egg’s weight, albumen (egg white) 

height, shell strength, vitelline (yolk) 

membrane strength, and Haugh unit. A 

Egg Quality Preserved After Exposure 

to Egg Crack Detection Technology

Haugh unit—considered by the egg industry as the “gold standard” of interior 

egg quality—is a mathematical formula 

that takes into account the egg’s weight 

and the height of the albumen.

“This information lets us know that the 

use of the modified-pressure imaging system to detect cracked eggs does not affect 

egg quality, making it an important tool 

for enhancing the safety of shell eggs for 

U.S. retail sale,” says Jones.—By Sharon 

Durham, ARS.

Deana Jones is in the USDA-ARS Egg 

Safety and Quality Research Unit, Richard 

B. Russell Research Center, 950 College 

Station Rd., Athens, GA 30605; (706) 

546-3486, deana.jones@ars.usda.gov.*

New Primer Helps Identify 

More DNA Markers

watermelon genes and could be used as 

primers. Levi and Wechter believed that 

these new primers would generate a larger 

number of markers because they are more 

targeted than random primers.

Zhangjun Fei, an ARS-funded bioinformatics researcher at the Boyce Thompson 

Institute for Plant Research in Ithaca, 

New York, collaborated with Levi and 

Wechter and wrote a computer script to 

identify oligonucleotides that exist in high 

numbers in genes of watermelon. They 

named the new primers “high-frequency 

oligonucleotides targeting active genes,” 

or HFO-TAG for short.

Working from the U.S. Vegetable 

Laboratory in Charleston, South Carolina, 

the scientists and fellow ARS and university colleagues tested their theory on 

12 closely related watermelon cultivars. 

The researchers found that the HFO-TAG 

primers identified more DNA fragments 

than random primers did. Finding more 

fragments means researchers have a greater 

chance of finding DNA markers for genes 

that control desirable traits. And they don’t 

have to invest as much time and money to 

identify the markers.

Levi and Wechter are currently using the 

HFO-TAG primers to look for watermelon 

genes that control disease or pest resistance 

and fruit quality. The primers will also be 

useful in genetic studies and genetic mapping of watermelon.

According to the scientists, this simple 

and straightforward method can be applied to genetic studies of other plants as 

well as animals. A full description of this 

study has been published in the Journal 

of the American Society for Horticultural 

Science.—By Stephanie Yao, formerly 

with ARS.

Amnon Levi and Pat Wechter are with 

the USDA-ARS U.S. Vegetable Laboratory, 2700 Savannah Hwy., Charleston, 

SC 29414; (843) 402-5326 [Levi], (843) 

402-5318 [Wechter], amnon.levi@ars.

usda.gov, pat.wechter@ars.usda.gov.*

DNAmarkers are important tools for 

identifying genes that control 

traits of interest to plant breeders, such as 

disease resistance or fruit quality. DNA 

markers are usually generated using “primers,” short segments of DNA that are used 

by geneticists to look for genes that control 

specific traits. In general, geneticists use 

random primers in their search for DNA 

markers, but that process is often long and 

arbitrary, and it can result in researchers 

spending a lot of time and money to identify 

just one DNA marker.

To streamline the process, Agricultural 

Research Service geneticist Amnon Levi 

and plant pathologist Pat Wechter have 

developed a new method for identifying 

DNA markers. They used genomic data 

to search for small pieces of DNA, called 

“oligonucleotides,” that are prevalent in 
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 51

wo researchers at the U.S. Horticultural Research Laboratory in Fort Pierce, Florida, are attracting international 

attention in diverse scientific fields for their approach 

to a common problem in science: how to predict every 

possible variable in an experiment where you simultaneously manipulate numerous components.

Researchers who use culture media to grow and study cells, 

tissues, or any biological entity typically try to optimize the 

media by varying one ingredient at a time, while holding all 

the other ingredients constant. The problem is that changing the 

amount of any single ingredient in a mixture changes not only 

the amount of that ingredient, but also its proportion to every 

other ingredient in the mix. The one-ingredient-at-a-time—or 

one-factor-at-a-time—approach fails to take into account the 

effects of proportions. In addition, this can be an expensive and 

time-consuming process, with no significant improvement in 

culture growth.

But geneticist Randall P. Niedz and ecologist Terence J. 

Evens have developed a new approach that can help researchers 

reformulate any type of mixture, whether it is a culture medium, 

fertilizer, potting soil, insect diet, or animal feed.

Niedz and Evens encountered the problem a few years ago 

while each was studying mineral nutrients. Niedz was trying to 

improve the growth of citrus tissue culture, an important area 

for crop improvement, but one that tends to be a challenge. 

Evens was studying the effects of algal growth in runoff from 

ornamental plants in nurseries.

A typical plant/algae culture medium contains about 16 individual mineral nutrient ions, and its effects are determined by 

both the amount and the proportion of each ingredient in the mix. 

Niedz and Evens recognized that creating a nutrient solution is 

a special type of mixture problem and should be defined by the 

composition of its individual ions. They found that by examining 

ions independent of their parent salts, they could make sense of 

the specific ion effects in their solutions.

The method they developed of reconfiguring a “recipe” is 

complex and must be done with a computer using both an algorithm they devised and experimental designs that separate out 

the effects of proportionality and amount. Results are teased out 

in ways that reveal every possible outcome and are considerably more accurate, resource efficient, and knowledge rich than 

results from standard one-ingredient-at-a-time approaches, the 

researchers say. When applied to citrus tissue and algal culture, 

the results were dramatic, saving time and money and enhancing 

cell growth. In the citrus experiments, growth of citrus tissue cultures increased nearly 200 percent. In the algal experiments, they 

found unusual mixtures where algae grew vigorously and at pH 

levels far beyond where traditional science said they should grow.

The approach developed by Niedz and Evens is being used 

not only by scientists in their fields, but also by entomologists, 

medical researchers, and even chemists around the world to 

gauge the effects of varying ingredients in mixtures. They explained the approach in a letter to Nature Methods in June 2006 

and a report in Scholarly Research Exchange in 

May 2008. They have also released a free online 

software package, for mineral nutrient research, 

that has been downloaded more than 300 times by 

scientists in 39 countries. The software package is 

available at www.ars.usda.gov/services/software/

download.htm?softwareid=148.—By Dennis 

O’Brien, ARS.

The research is part of Water Availability and 

Watershed Management, an ARS national program 

(#211) described at www.nps.ars.usda.gov. 

Randall P. Niedz and Terence J. Evens are 

with the USDA-ARS U.S. Horticultural Research 

Laboratory, 2001 South Rock Road, Fort Pierce, 

FL 34945; (772) 462-5919, randall.niedz@ars.

usda.gov, (772) 462-5921, terence.evens@ars.

usda.gov. X

Geneticist Randall Niedz (left) and ecologist Terence Evens inspect 

two green algae cultures for an ongoing study of the effects of 

fertilizers on algal growth.

Citrus cell lines growing on standard media formulation (left) and on a formulation 

identified after a single experiment using the new ion-based approach. The cells on 

the new formulation are growing almost 200 percent faster. The new approach can 

be used to make better formulations for many things, including potting soils, animal 

diets, fertilizer blends, and algae nutrient solutions. 

PETER D’AIUTO (D1796-1)

ELDRIDGE WYNN (D1785-1)

A New Approach to an Old 

Problem: Devising Formulas 

To Enhance Growth

ELDRIDGE WYNN (D1786-1)

T
52 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

production facility in the United States.

Meanwhile, in Raleigh, North Carolina, Marshall 

coordinates the regional winter barley testing nursery, which has the best experimental lines from both 

public and private winter barley breeding programs in 

the United States. He and other scientists in the ARS 

Plant Science Research Unit are just a few years into 

making crosses between hull-less barley and barley 

with resistance to Ug99, a stem rust that can inflict 

crop losses of up to 100 percent.

Once the researchers have developed robust lines 

that contain both traits, they’ll begin breeding for traits 

to enhance ethanol production, such as starch content. 

“In several years, we hope to release barley varieties 

with traits for enhanced agronomic performance, good 

grain-to-ethanol qualities, and good resistance to stem 

rust,” Marshall says.—By Ann Perry, ARS.

This research is part of Plant Genetic Resources, 

Genomics, and Genetic Improvement (#301), Bioenergy and Energy Alternatives (#307), and Quality and 

Utilization of Agricultural Products (#306), three ARS 

national programs described at www.nps.ars.usda.gov.

Kevin B. Hicks is with the USDA-ARS Crop Conversion Science and Engineering Research Unit, 

Eastern Regional Research Center, 600 E. Mermaid 

Lane, Wyndmoor, PA 19038; (215) 233-6579, kevin.

hicks@ars.usda.gov.

 David S. Marshall is in the USDAARS Plant Science Research Unit, 

North Carolina State University, 

3411 Gardner Hall, Raleigh, NC 

27695; (919) 515-6819, david.

marshall@ars.usda.gov. X

Boosting Barley for Bioenergy

BARLEY

OATS &

Hulled winter barley ready for harvest. 

gricultural Research Service (ARS) scientists 

Kevin Hicks and David Marshall want winter 

barley to become a prime-time player in bioenergy production.

“The 2007 Energy Independence and 

Security Act requires production and use of 36 billion 

gallons of renewable transportation fuels by 2022. 

Today we only make 9 billion,” says Hicks. “We see 

winter barley as the perfect biofeedstock for making 

biofuels on the East Coast.”

So Hicks and others in the ARS Crop Conversion 

Science and Engineering Research Unit in Wyndmoor, 

Pennsylvania, are developing new sustainable technologies to convert varieties of hulled and hull-less 

winter “energy” barley into fuel ethanol. This initiative 

also includes Virginia Polytechnic Institute and State 

University scientists Carl Griffey, Wynse Brooks, and 

Mark Vaughn, who are supervising ongoing research 

efforts to develop improved varieties of hulled and 

hull-less barley.

Their combined efforts could help farmers from 

southern Pennsylvania to South Carolina develop a 

profitable 2-year rotation of winter barley, corn, and 

soybeans. Winter barley is grown on seasonally fallow land. It acts as a cover crop by protecting soil and 

nutrients and preventing migration of fertilizers from 

crop fields to the Chesapeake Bay—which is why the 

Chesapeake Bay Commission supports the development 

of winter barley as an energy crop. And since the field 

would otherwise be left fallow, producing biofuels from 

winter barley would not interfere with food production.

Now, too, there is a major marketing opportunity 

for growers of winter barley. Osage Bio Energy, 

headquartered in Glen Allen, Virginia, is well under 

way in constructing the first major barley-to-ethanol 

A

BILL SCRUGGS (D1661-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 53

he stem rust fungus Puccinia graminis has long plagued 

the world’s wheat, barley, and other grain crops. But 

none of the fungus’s main types have matched the 

devastation wrought by Ug99. It’s a virulent new race 

that even stem rust-resistant varieties cannot withstand. 

So pressing is the threat posed by Ug99, known scientifically 

as “Puccinia graminis f. sp. tritici,” that the Agricultural Research Service has committed multiple labs to the global fight 

against the pathogen. ARS’s efforts also support the Borlaug 

Global Rust Initiative, an international effort to rush newly 

developed rust-resistant cultivars to affected wheat growers, 

whether they be in regions where Ug99 already occurs—namely, 

parts of North Africa and the Middle East—or areas it could 

spread to next.

The labs, followed by summaries of their Ug99 research, 

include:

Cereal Disease Laboratory, St. Paul, Minnesota—

Characterizes and monitors Ug99 and other emerging rust 

strains; tests breeding germplasm of U.S. wheat and barley for 

resistance to Ug99 in the greenhouse; identifies new sources of 

resistance in cultivated and wild relatives of wheat; develops 

molecular markers; and creates genetic maps of Ug99 and other 

important rust strains. (See “World Wheat Supply Threatened!” 

Agricultural Research, November/December 2007, pp. 4-6.)

Plant Science Research Unit, Raleigh, North Carolina—

Coordinates Ug99 screening of U.S. wheat and barley submissions at the Njoro Research Center of the Kenya Agricultural 

Research Institute; developed wheat lines with multiple genes 

for resistance to Ug99 and other stem rusts; and identified resistance sources in several barley lines being tested in Kenya. (See 

“International Wheat and Barley Screening Collaboration Helps 

Uncover Stem Rust-Resistant Material,” Agricultural Research,

February 2010, pp. 8-9.)

Small Grains and Potato Germplasm Research Unit, 

Aberdeen, Idaho—Coordinates acquisition and shipping of 

seed from wheat breeders across the United States for testing 

in Kenya; prescreens landrace wheats from the National Small 

Grains Collection against local stem rust races; and crosses 

resistant landraces tested in Kenya to study inheritance in offspring as part of the effort to discover new resistance genes. (See 

“International Wheat and Barley Screening Collaboration Helps 

Uncover Stem Rust-Resistant Material,” Agricultural Research,

February 2010, pp. 8-9.)

Cereal Crops Research Unit, Fargo, North Dakota—

Identified novel sources of stem rust and Ug99 resistance in rye, 

goat grasses, perennial wheat grasses, and other wild species; 

and combined classical cytogenetics with molecular marker 

techniques to develop bread and durum wheat lines carrying 

resistance genes derived from wild relatives of wheat, including 

Sr37, Sr39, Sr43, and Sr47, that are free of “linkage drag”—unwanted segments of chromosome that can be inherited from wild 

species along with rust resistance genes, hindering commercial 

breeding efforts.

Hard Winter Wheat Genetics Research Unit, Manhattan, 

Kansas—Identified four new resistance genes from wild 

relatives of wheat to combat Ug99 and developed genetic stocks 

for their use in wheat breeding; developed genetic markers and 

improved germplasm for several Ug99-effective resistance genes, 

including Sr22, Sr35, and Sr40; used chromosome-engineering 

techniques to shorten introduced chromosome segments from 

wild relatives of wheat and thus reduce undesirable linked 

characters; and use marker-assisted selection to move useful 

resistance genes into elite hard winter wheat varieties for Central 

and Southern Plains breeders.—By Jan Suszkiw, ARS.

This research is part of Plant Genetic Resources, Genomics, 

and Genetic Improvement (#301) and Plant Diseases (#303), 

two ARS national programs described at www.nps.ars.usda.gov.

To reach scientists involved in these projects, contact Jan 

Suszkiw, USDA-ARS Information Staff, 5601 Sunnyside Ave., 

Beltsville, MD 20705-5129; (301) 504-1630, jan.suszkiw@ars.

usda.gov. X

Wheat

T

Ug99-infected wheat from a nursery in Njoro, Kenya. 

YUE JIN (D1797-1)

ARS Wheat Rust Resistance Roundup
54 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

A citrus leafminer

larva creates a gallery, 

or mine, within a 

citrus leaf, thereby 

gaining protection 

from externally applied 

pesticides and leaving

behind a fecal trail. The 

wound created by the 

larva also makes the 

plant more susceptible 

to citrus canker disease.

ARS research leader David Hall (left) observes 

as entomologist Stephen Lapointe applies 

a formulation of SPLAT containing the sex 

pheromone of the citrus leafminer.

PEGGY GREB (D1853-1)

A 1-gram dollop of 

SPLAT containing 

the sex pheromone 

to disrupt citrus 

leafminer mating.

PEGGY GREB (D1851-1)

developed treatments that throw males 

off the scent of fertile females in orchards 

and fields. The technique has been used to 

control gypsy moths, codling moths, and 

several other pests that attack fruit and 

vegetable crops. These treatments are considered environmentally friendly because 

they reduce the need for insecticides and 

are designed to target specific pests. “In all 

of them, we are basically just interfering 

with the male’s ability to receive the signal 

from the female,” Lapointe says.

Lapointe is working with Lukasz Stelinksi of the University of Florida’s 

Citrus Research and Education Center to 

see whether they can disrupt leafminer 

mating by manipulating either of two 

compounds—a triene and a diene—used 

by female leafminers to attract mates.

The researchers set out to examine 

whether the formulation of three parts 

triene to one part diene would be optimal 

for attracting males in a trap. They also 

wanted to see what formulations would 

be most effective at confusing males and 

disrupting their ability to pick up the 

female scent.

The researchers created synthetic female-scented traps, placed them in a citrus 

grove, and counted the number of males 

caught. They confirmed that the three-toone ratio of triene to diene worked better 

than triene or diene alone as an attractant. 

In 2.5 months, more than 48,000 males 

were captured in traps baited with the 3:1 

blend compared with around 3,500 males 

Agricultural Research Service scientists 

are working on controlling a pest that 

poses an increasing threat to Florida 

citrus groves by exploiting the insect’s 

own reproductive habits. 

The leafminer moth, Phyllocnistis 

citrella, forms channels as it feeds inside 

citrus leaves and, as a result, often makes 

the plant more susceptible to canker disease. Further exacerbating the leafminer 

problem is the spraying of more insecticide to combat another pest—the Asian 

citrus psyllid. The insecticide is killing off 

the leafminers’ natural enemies, allowing 

the pest to increase in numbers.

Commercial traps can sometimes help, 

but Stephen Lapointe, an ARS entomologist with the U.S. Horticultural Research 

Laboratory in Fort Pierce, is exploring a 

control strategy that has proved effective 

with other pests: mating disruption.

Many insects release pheromones to 

attract mates. In some cases, scientists 

have synthesized those pheromones and 

captured in traps baited with the triene 

and only 70 in traps baited with the diene.

In a second phase of the project, the 

researchers surrounded the female-scented 

traps with 17 different combinations of 

the two synthetic compounds—as well 

as each compound on its own—to see 

which would be most effective at preventing males from finding the traps. They 

placed the experimental treatments around 

female-scented traps at different points inside a 59-acre grove of grapefruit trees. If 

the experimental treatments prevented the 

males from reaching the female-scented 

traps, the males theoretically would be 

unable to find females in natural settings, 

the researchers say. They used a waxy 

substance known as “SPLAT” that slowly 

released the experimental treatments over 

time, and they checked once a week over 

several months to see which treatments 

were most effective at keeping leafminers 

out of the female-scented traps.

Results showed that either compound 

used alone was as effective as the 3:1 

blend at keeping male leafminers away 

from the female-scented traps. The dieneonly treatment resulted in an 89-percent 

reduction in moth catches, and the trieneonly treatment resulted in an 83-percent 

reduction. Greater amounts of diene are 

required to disrupt the moths, but diene is 

also much cheaper to synthesize, Lapointe 

says. 

The work was recently published in the 

Journal of Chemical Ecology. Lapointe 

is also working with ISCA Technologies, 

Inc., of Riverside, California, a manufacturer of the SPLAT technology, to use 

these results to develop a marketable 

leafminer mating-disruption technology.—By Dennis O’Brien, ARS.

The research is part of Crop Protection and Quarantine, an ARS national 

program (#304) described at www.nps.

ars.usda.gov.

Stephen Lapointe is in the USDA-ARS 

Horticultural Research Laboratory, 2001 

South Rock Rd., Fort Pierce, FL 34945; 

(772) 462-5914, stephen.lapointe@ars.

usda.gov. *

Throwing a

CITRUS PEST

PEGGY GREB (D1852-1)

Off Its Scent
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 55

Newcastle disease virus (NDV) is an 

important pathogen that causes disease and 

death not only in domestic and commercial 

poultry, but also in wild bird populations 

around the world. Current Newcastle 

disease (ND) vaccines are used widely 

in commercial poultry and protect the 

vaccinated birds from disease but do not 

prevent them from becoming infected and 

carrying the virulent virus or shedding it in 

their feces. Therefore, the current vaccines 

do not eliminate virulent virus transmission 

from infected to healthy birds. 

A vaccine that reduces virulent virus 

shed and transmission is sorely needed by 

the poultry industry.

Using reverse genetics technology, 

researchers in the Endemic Poultry Viral 

Disease Research Unit and the Exotic and 

Emerging Viral Diseases Research Unit of 

the Southeast Poultry Research Laboratory 

in Athens, Georgia, have developed a new 

vaccine from parts of a virus that is similar 

to the wild-type NDV circulating in the 

environment today. This new vaccine not 

only reduces mortality and severity of ND 

symptoms in poultry, but it also decreases 

the amount of virulent virus shed from 

vaccinated birds.

“Currently, most vaccines used in the 

United States are formulated with NDV 

isolated in the 1940s, which is similar 

to the virulent NDV circulating at that 

time,” says poultry unit microbiologist 

Qingzhong Yu. “Unfortunately, with time, 

new NDV strains have emerged that are 

genetically very different from commonly 

used vaccine strains.

“Reverse genetics technology enabled 

us to generate a new vaccine by exchanging a gene from the original vaccine with 

a similar gene of the current circulating 

virus. We found that when the new vaccine, 

containing gene sequences similar to the 

wild-type virus, was used in vaccination 

studies, the vaccinated birds were protected 

from disease and shed less of the wild-type 

virus after challenge,” says Yu.

Yu, Daniel King (retired ARS researcher), David Suarez, Patti Miller, and former 

ARS researcher Carlos Estevez (now with 

Texas A&M) submitted a patent application for the vaccine in 2009. Licensing 

by the USDA Animal and Plant Health 

Inspection Service’s Center for Veterinary 

Biologics would have to follow before the 

vaccine could be used.

NDV causes disease in more than 250 

species of birds and typically affects 

the respiratory, gastrointestinal, and/or 

nervous system. Symptoms may include 

gasping, coughing, lack of appetite, drooping wings, and diarrhea. ND is clinically 

similar to avian influenza, and the two 

diseases may be confused, which impairs 

the rapid diagnosis of a disease outbreak.

The most severe form of ND can result 

in disease and mortality rates exceeding 90 

percent in susceptible chickens. The most 

recent U.S. outbreak—which occurred in 

2002-2003 in California, Nevada, Arizona, 

and Texas—illustrates the devastation and 

financial cost that can result: More than 3.4 

million birds were destroyed, and the cost 

of controlling the outbreak in California 

alone was more than $160 million. 

“Newcastle disease continues to be a 

danger to the commercial poultry industry 

because it can spread rapidly and can exact 

a heavy toll,” says Yu. “Vaccines for ND 

have been used for more than 50 years 

to control the disease and are successful 

in reducing mortality and the severity of 

symptoms. Our goal is to create a vaccine 

to decrease virus spread as well.”—By 

Sharon Durham, ARS.

This research is part of 

Animal Health, an ARS 

national program (#103) 

described at www.nps.

ars.usda.gov.

Qingzhong Yu is in 

the USDA-ARS Endemic 

Poultry Viral Disease Research Unit, 934 College 

Station Rd., Athens, GA 

30605; (706) 546-3628, 

qingzhong.yu@ars.usda.

gov.*

Newcastle Disease Virus 

Vaccine on the Horizon

Microbiologist Qingzhong Yu examines recombinant Newcastle disease virus vaccine candidates 

in infected cells.

PEGGY GREB (D2048-1)
56 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

I

n the United States, parasitic infections contribute to losses of more 

than $2 billion annually in livestock 

alone. In turn, some parasites, like 

tapeworm, can infect humans who eat 

uncooked or undercooked beef or pork.

Fortunately, ARS maintains archival 

collections of parasites for research, identification, and diagnostic purposes, the 

vast majority of which are held at the U.S. 

National Parasite Collection (USNPC), 

which is curated by ARS zoologist Eric 

Hoberg.

Hoberg is with the Animal Parasitic 

Diseases Laboratory, which is part of the 

Henry A. Wallace Beltsville Agricultural 

Research Center in Beltsville, Maryland. 

The collection was established in 1892 and 

is among the largest parasite collections 

in the world. 

Current holdings include more than 

20 million catalogued specimens representing nematodes, tapeworms, flukes, 

spiny-headed worms, and some parasitic 

arthropods, such as fleas, ticks, and lice. 

Detailed biodiversity information about 

hosts and geographic distribution is maintained in an on-line database.

The USNPC contributes significantly to 

explorations of diversity, evolution, and 

distribution, furthering our understanding 

of the socioeconomic and ecological 

significance of parasites and pathogens. 

Archival collections serve as critical 

baselines to understand ecological 

disturbance. Archives provide a foundation 

to identify shifting geographic and host 

ranges for parasites and diseases that may 

emerge with accelerated global change.

Newly Reclassified Protozoa at Work

ARS researchers have also assembled 

and maintain invertebrate protist collections at three research locations for the 

purpose of in-house and joint projects.

At the Center for Medical, Agricultural, 

and Veterinary Entomology (CMAVE), in 

Gainesville, Florida, researchers are using 

a collection of microsporidia—formerly 

classified as protozoa and now considered 

fungi—to act as soldiers of biological 

Archiving Parasites and Protozoa for 

Research, Diagnoses, and More

warfare at the tiniest level. Species of 

these spore-producing parasites, such as 

Kneallhazia solenopsae, are being used 

to bring about declines in red imported 

fire ant (Solenopsis invicta) populations. 

In Argentina, these infectious soldiers 

are associated with localized declines 

of 53 percent to 100 percent in fire 

ant populations, according to CMAVE 

entomologist David Oi.

In addition, Oi and CMAVE colleagues 

Sanford Porter and Steven Valles were 

able to get K. solenopsae to infect phorid 

flies without harming them. That’s important because the flies may serve as vectors 

to infect red imported fire ants with the 

microsporidia—perhaps facilitating the 

spread of infection to other colonies.

K. solenopsae not only reduces fire ant 

colony size, it also reduces the number of 

reproducing ants, decreases the survival 

of queens, and increases the mortality 

rate of colonies, says Oi. The collection 

enables scientists to research the potential 

for using these and other microbes as 

biocontrol agents.

In Sidney, Montana, ARS scientists at 

the Northern Plains Agricultural Research 

Laboratory used the U.S. Rangeland 

Grasshopper Collection’s microsporidia 

holdings to develop the first microbial 

control agent registered for use in the 

United States against grasshoppers. Largescale outbreaks of grasshoppers occur 

about every 8 to 10 years. In 2001, such an 

outbreak caused an estimated $25 million 

of damage to crops in Utah alone.

And researchers at the Grain Marketing 

and Production Research Center in 

Manhattan, Kansas, maintain protozoa 

in a collection that is used to develop 

biocontrol agents against beetles and 

other bugs that burrow into stored grain 

products.—By Rosalie Marion Bliss and

Sharon Durham, ARS.

This research is part of Animal Health, 

an ARS national program (#103) described at www.nps.ars.usda.gov.

Eric P. Hoberg is in the USDA-ARS 

Animal Parasitic Diseases Laboratory, 

10300 Baltimore Ave., Bldg. 1180, Beltsville, MD 20705-2350; (301) 504-8588, 

eric.hoberg@ars.usda.gov.

David Oi is in the USDA-ARS Center 

for Medical, Agricultural, and Veterinary 

Entomology, 1600 S.W. 23rd Dr., Gainesville, FL 32608; (352) 374-5987, david.

oi@ars.usda.gov. X

Entomologist David Oi collects infected fire 

ants from a colony decimated by the fire ant 

pathogen Kneallhazia solenopsae. 

Eric Hoberg, chief curator of the U.S. 

National Parasite Collection, examines 

roundworm specimens from raccoons, which 

pose a potential threat for human infection. 

PEGGY GREB (D1578-1)

PEGGY GREB (K10225-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 57

Troublesome Microbes That Resist Antimicrobials 

The Antimicrobial Resistance Collection

In an effort to monitor pathogenic microbes’ resistance to antimicrobials, 

the National Antimicrobial Resistance Monitoring System (NARMS) was 

established in 1996 by the U.S. Food and Drug Administration’s Center for 

Veterinary Medicine in collaboration with the Centers for Disease Control 

and Prevention and the U.S. Department of Agriculture.

The animal component of NARMS focuses on zoonotic pathogens (those 

that can be transferred from livestock or wildlife to humans) and is housed 

within ARS’s Bacterial Epidemiology and Antimicrobial Resistance Research 

Unit. Led by microbiologist Paula Cray, the unit is part of the ARS Richard 

B. Russell Research Center in Athens, Georgia.

The NARMS animal 

component tests 

samples, or isolates, obtained from 

healthy on-farm 

animals, animals 

being diagnosed for 

illness, and food 

animals at slaughter. The specimens 

are stored in the 

Antimicrobial Resistance Collection, maintained by 

Cray’s team.

Resistance of 

Salmonella, Campylobacter, Enterococcus, and Escherichia coli to antimicrobials such as streptomycin and tetracycline is tested, monitored, 

and tracked in an attempt to better understand foodborne pathogens’ 

resistance trends.

“Nontyphoid Salmonella was chosen as a sentinel organism of NARMS’s 

animal component, which was launched in 1997,” says Cray. A sentinel 

organism is one used to track changes in resistance over time. “Testing of 

Campylobacter isolates began in 1998, while E. coli was included in 2000. 

Enterococcus testing has also been added to the data set.

“It is vital that we track these trends of resistance and disseminate the 

information to animal producers, veterinarians, and consumers.”—By 

Sharon Durham, ARS.

Paula Cray is in the USDA-ARS Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Richard B. Russell Research Center, 950 

College Station Rd., Athens, GA 30605; (706) 546-3685, paula.cray@

ars.usda.gov.

Research leader Paula Cray (left) and 

technician Lori Ayers perform antimicrobial 

susceptibility testing on a bacterial culture. 

PEGGY GREB (D602-1)

Experiments by Agricultural Research Service scientists at 

Raleigh, North Carolina, and Urbana, Illinois—and their university colleagues—have shown that future higher levels of 

ozone may cancel out some of the benefits to crops expected 

from higher carbon dioxide (CO2) levels.

For one thing, crops wouldn’t achieve the 30-percent increase 

in photosynthesis—and resulting higher yields—expected as 

CO2

 levels continue to rise.

The scientists have also found that ozone can thwart expected 

high CO2 benefits by lowering crop quality. It can also help 

invasive weeds outcompete forage and other crops.

“We are beginning to look at interactions between ozone 

and diseases such as stripe rust and stem rust of wheat,” 

says David Marshall, research leader of the Plant Science 

Research Unit at Raleigh, and an expert on wheat rusts.—By 

Don Comis, ARS.

Ozone Erodes CO2 Benefits for Plants

PEGGY GREB (D1548-1)

Plant physiologist Fitzgerald Booker prepares to place an optical 

scanner into a tube positioned in the soil to photograph soybean 

roots. The photos will show changes in root growth caused by 

elevated carbon dioxide and ozone, pumped into the open-top 

field chambers.
58 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

has bred 

soybeans for the Agricultural Research Service for 30 years, but for the last couple of 

years, he has been trying to solve a mystery: 

Why do the world’s most stress-resistant 

soybean types hail from a little village in 

far-northern Sweden? 

Stress resistance is a rare commodity in 

soybean, but these Swedish varieties put 

up with a host of problems—drought, iron 

deficiency, toxic soil aluminum and salts, 

and even high levels of ozone. 

Although Sweden is not known for its 

soybean production, Swedish breeders 

made a major breakthrough—but one that 

went unnoticed for decades by the soybean 

community and even by the breeders. 

“We now know that they did something 

very right. The mystery is how,” Carter says.

Carter, who is in the ARS Soybean and 

Nitrogen Research Unit at Raleigh, North 

Carolina, has long been interested in breeding for stress resistance. Ozone resistance 

has become his most recent interest, in large 

part because of his collaboration with ozone 

expert Kent Burkey, a plant physiologist 

in the ARS Plant Science Research Unit 

at Raleigh.

Their stress studies led the scientists to 

the treasure trove of genetic resistance in 

Swedish soybeans, which appear to have an 

even more pronounced resistance to ozone 

than to the other stresses. Understanding 

the ozone effect may be a key to unraveling 

the secrets of the broad stress resistance of 

the Swedish soybeans.

Tracing the American Soybean’s 

Family Tree

Carter uncovered the resistance mystery 

after analyzing thousands of soybean 

types to generate the family tree of North 

American soybeans. From this, he found 

30 ancestors, which together account for 

92 percent of the genetic material in North 

American soybeans.

Carter screened these ancestors first 

for salt tolerance. He found two lines of 

vegetable soybeans—Fiskeby 840-7-3 

and Fiskeby III, both from the Swedish 

village of Fiskeby—that were the most salt 

tolerant. Then he screened for aluminum 

tolerance, and again the Fiskeby plants 

stood out.

“Then, my colleagues and I saw the 

same thing with drought tolerance and 

ozone” and realized a pattern had emerged, 

Carter says.

ARS scientists in Raleigh and in Urbana, 

Illinois, study how increases in atmospheric 

greenhouse gases, particularly carbon dioxide and ozone, will affect crops, especially 

soybeans and wheat.

To screen the ancestors for ozone tolerance in a 2003 to 2005 study, Carter turned 

to Burkey for help. The two scientists 

combined the results of this study with 

breeder pedigree records and found that 

only a few U.S. cultivars trace their ancestry to the Fiskeby stress-tolerant types. 

“This indicates that there is great potential 

to increase tolerance to ozone and other 

stresses in North American soybeans by 

adding genes from Fiskeby,” Burkey says.

He and Carter and Jim Orf, a soybean 

breeder/geneticist at the University of MinSoybean breeder and geneticist Tommy Carter inspects research plots during extreme drought stress at the North Carolina State Sandhills Research 

Station. Carter evaluates approximately 25 acres (5,000 plots) of soybean for drought/stress resistance annually. 

USDA-ARS (D2226-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 59

nesota at St. Paul, have crossed Fiskeby III 

with ozone-susceptible Mandarin Ottawa 

and developed 240 breeding lines from the 

offspring. With the help of funding from 

the United Soybean Board, in Chesterfield, 

Missouri, the team is mapping the genes 

in these lines to see which genes are connected to resistance to ozone and the other 

stresses.

“This approach can be applied to other 

soybean-producing regions such as China, 

Brazil, and Europe,” says Burkey. “Their 

breeding programs, in turn, may offer us 

other important germplasm to explore for 

ozone tolerance genes.”

Cell Wall the First Line of 

Ozone Defense

Ozone enters leaf stomata as a gas and 

then dissolves in the liquid layer, called 

the “apoplast,” that surrounds plant cells. 

The apoplast is considered the first line of 

defense against pollutants, where ozone 

can be detoxified before it reaches the 

leaf cell surface and causes the damage 

that interferes with photosynthesis and 

reduces yields.

In the search for ways to improve crop 

ozone tolerance, Burkey and Cosima 

Wiese—associate professor of biology 

at Misericordia University in Dallas, 

Pennsylvania—recently began studying 

Fiskeby to see whether leaf apoplast 

antioxidants might be at least part of 

Fiskeby’s defense against ozone. Burkey 

and others have found that, in certain other 

species, vitamin C plays a role in keeping 

ozone from penetrating through the cell’s 

first line of defense. But soybean contains 

little vitamin C in the leaf apoplast, so they 

are looking for other antioxidants that may 

play a role.

Breeding Ozone-Tolerant Crops

ARS scientists in Urbana are taking a 

slightly different, but complementary, approach to the work of the Raleigh scientists. 

They are using SoyFACE (Soybean Free 

Air Concentration Enrichment) to screen 

soybean varieties for ozone tolerance and 

sensitivity. SoyFACE involves testing 

plants in open-air field conditions, under 

atmospheric conditions predicted for the 

year 2050. At that time, ozone concentrations are expected to be 25-50 percent 

higher than today’s concentrations.

The work is being done by molecular 

biologist Lisa Ainsworth, Amy Betzelberger, a graduate research assistant in the 

Department of Plant Biology at the University of Illinois at Urbana-Champaign, 

and geneticist Randall Nelson and other 

ARS colleagues at Urbana.

During 2007 and 2008, the team tested 

10 soybean varieties that had been released 

between 1952 and 2003. These were selected from initial tests of 22 cultivars and 

experimental lines that had been evaluated 

for 4 years. The scientists found that, on 

average, exposure to 

82 parts per 

Ozone is a greenhouse gas found 

in smog. It is formed mostly when 

sunlight “cooks” automotive and industrial pollutants that originate from 

combustion of carbon-based fuels.

Ozone is the most damaging air 

pollutant to plants.

Fitz Booker, an Agricultural Research Service plant physiologist 

at the Plant Science Research Unit 

at Raleigh, North Carolina, says, 

“Ozone has long been known to 

affect a wide range of plants, including grasses, field crops, horticultural 

crops, and forests. Our research and 

that of other scientists has shown 

that many crops and forages are 

damaged by high ozone levels, 

including soybeans, wheat, cotton, oats, potatoes, rice, peanuts, 

tomatoes, grapes, alfalfa, clover, 

and barley.”

In fact, during the 1950s, Howard 

Heggestad (deceased) discovered 

that what were thought to be symptoms of a plant disease on tobacco 

leaves in the smoggy Connecticut 

River Valley was actually damage 

from ozone. In the Washington, 

D.C., area, he found similar damage 

to plants from ozone in smog. At the 

time, Heggestad was an ARS plant 

pathologist.

Globally, yield losses from ozone 

have been estimated at $14 to $26 

billion for rice, soybean, corn, and 

wheat combined.—Don Comis, 

ARS.

At the ARS Soybean and Nitrogen Research unit 

in Raleigh, North Carolina, Tommy Carter (right)

and plant physiologist Kent Burkey 

examine a Fiskeby soybean 

ancestor being placed in 

greenhouse exposure 

chambers to assess its 

ozone injury response.

Ozone:

Plants Don’t Like It

AMY BURTON (d2252-1)
60 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

billion (ppb) ozone reduced soybean yields 

by 23 percent in 2007, and exposure to 61 

ppb reduced yields by 12 percent in 2008. 

They found significant differences in ozone 

tolerance among the 10 varieties. “But we 

didn’t see any significant improvement 

in ozone tolerance in soybean varieties 

released after the 1980s,” Ainsworth says. 

This again shows the potential and need 

for breeding more ozone-tolerant varieties.

Ozone Damage Seen From Above

In a 2002 to 2006 study led by the 

National Aeronautics and Space Administration, NASA scientists, Ainsworth, ARS plant physiologist 

Fitz Booker, and university scientists investigated widespread 

ozone damage to soybeans in 

Iowa, Illinois, and Indiana using 

ozone surface monitors, satellite instruments, and historical 

yield data. Ainsworth says that 

satellite information is useful for 

investigating ozone’s impacts 

on crop yields in areas without 

ground-monitoring networks, 

such as rural regions. “Satellite 

observations of farmland in 

other countries could provide 

important insight into the global 

ARS scientists Carl Bernacchi (left), 

Don Ort (center), and Lisa Ainsworth 

in a plot of soybeans treated with 

elevated carbon dioxide at the 

SoyFACE Global Change Research 

Facility at the University of Illinois 

Research Farm in Urbana. 

To assess oxidative stress in soybeans grown at 

SoyFACE under elevated ozone concentrations, 

ARS molecular biologist Lisa Ainsworth (back) 

and graduate student Kelly Gillespie use a liquidhandling robot to perform a high-throughput 

assay. 

PEGGY GREB (D1550-1)

extent of this problem,” she adds.

In the study, the scientists found that 

ozone levels above 50 ppb could reduce 

yields by about 10 percent in the Midwest 

Corn Belt, costing more than $1 billion in 

lost crop production.

Their findings are consistent with those 

from their SoyFACE studies and studies 

in outdoor open-top chambers.

Ozone levels in most urban areas of 

the United States have declined with 

improvements in emission controls. 

But ozone levels are expected to rise in 

countries like India and China, as growing 

populations are able to afford more cars 

and build more power plants. Another 

concern is that ozone levels will rise in 

developing countries, where people can 

least withstand losses of staple crops such 

as rice and wheat.

“All this research promises to give breeders the tools they need to help farmers by 

providing them with more ozone-hardy 

crop varieties. This is great science with 

a solid application, the goal of all ARS 

research,” Carter says.—By Don Comis,

ARS.

This research supports the USDA priority of responding to climate change and is 

part of Climate Change, Soils, and Emissions (#212) and Plant Genetic Resources, 

Genomics, and Genetic Improvement 

(#301), two ARS national programs described at www.nps.ars.usda.gov.

To reach scientists mentioned in this 

story, contact Don Comis, USDA-ARS 

Information Staff, 5601 Sunnyside Ave., 

Beltsville, MD 20705-5129; (301) 504-

1625, donald.comis@ars.usda.gov.

*

Photo by Institute for Genomic Biology/University of Illinois (D1546-2)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 61

for vegetable,strawberry, deciduous fruit, 

nursery, and ornamental growers in their 

efforts to combat soil-dwelling nematodes, 

diseases, and weeds. But the fumigant is 

being phased out because of its harmful effects on the Earth’s protective stratospheric 

ozone layer, and alternative fumigants are 

presenting new challenges for growers and 

regulatory officials who want to keep the 

air clean.

The Agricultural Research Service has 

been conducting research to find the best 

alternatives to the fumigant since the mid1990s, and because of the issue’s critical 

importance, the agency initiated a special 

areawide pest-management project 5 years 

ago that made several additional research 

efforts possible. As part of that 5-year 

effort, ARS researchers in Florida and 

California are helping to minimize release 

of the alternative fumigants into the atmosphere with studies focused on fumigant 

emission rates and the effectiveness of 

tarps used as barriers to cover fumigated 

soil. The work also is designed to assist 

the U.S. Environmental Protection Agency 

(EPA) and other regulators charged with 

developing new fumigant requirements to 

better protect people who use them or live 

near treated fields.

Under requirements being imposed by 

EPA, growers who use fumigants will 

need to establish buffer areas around 

treated fields to protect neighbors from 

excessive exposure and develop detailed 

management plans that include either fumigant monitoring or notifying neighbors 

of fumigant applications. Experience in 

California suggests that many growers 

and pesticide applicators have been able 

to adapt to these types of fumigant requirements within about a year. But many 

smaller operations, particularly those near 

suburbs, may be unable to meet the proposed standards because of their proximity 

to homes, institutions, and public rights-of 

way. These include some California strawberry growers and south Florida growers 

of tomatoes, peppers, and cucumbers, says 

Dan Chellemi, an ARS plant pathologist at 

the U.S. Horticultural Research Laboratory 

in Fort Pierce, Florida.

The financial implications could be significant. In Florida, for instance, tomatoes 

were a $622 million crop in 2008, and bell 

peppers were valued at $267 million.

Field studies conducted by Chellemi, 

Husein A. Ajwa, a former ARS scientist 

now with the University of CaliforniaDavis, and colleagues, showed that 

implementation of recently developed application equipment and methods reduced 

emissions to levels far below those found 

in previous studies. “We found that the 

differences were quite significant,” Chellemi says.

Chellemi and colleagues applied several 

alternative fumigants under commercial 

application conditions at three sites near 

Duette, Florida, and three sites near Tifton, 

Georgia. The fumigants included chloropicrin, metam sodium, metam potassium, 

Helping Growers Adapt to Changing 

Rules on Fumigants

In a fumigated, tarped field in Tifton, Georgia, (left to right) horticulturist Jerry Johnson, plant 

pathologist Randy Driggers, and technicians Taylor Ivy and Nick Rotindo collect soil and air 

samples for analysis of chemical fumigants. Samples were collected to evaluate the impact of good 

agricultural practices on the soil fate and atmospheric emission of chemical fumigants.

Dan ChellEmi (D2246-1)

The vertical air-monitoring station located in the center of a fumigated field at a Duette, Florida, 

site is designed to continuously collect air samples at several heights. Fumigant-collection tubes 

were exchanged and air-sampling pumps calibrated every 6-12 hours for 10 consecutive days to 

ascertain fumigant flux rates from soil.

DAN CHELLEMI (D2247-1)
62 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

dimethyldisulfide, and 1,3-dichloropropene (sold as Telone). The fumigants 

were injected into the soil using shanks 

and low-disturbance coulters mounted 

on tractors, application methods that are 

becoming standard practice. The soil was 

then immediately covered with plastic 

tarps designed to prevent the fumigant 

from escaping.

The researchers used different types of 

plastic tarps, selected sites that included 

different soil types, and recorded the temperatures and moisture levels of the soil 

at times when the fumigants were applied. 

They also set up weather stations to monitor wind speeds and air sampling stations 

to track emission levels.

They found that emission rates could 

be drastically affected by the quality of 

the soil and the type of covering used. Coverings include 

tarps made with polyethylene 

or metal and VIF’s (virtually 

impermeable films), which 

have layers of nylon or other 

materials imbedded in them. 

The researchers found that 

in dry soils with low organic 

matter content, VIFs worked 

best at keeping emissions low, 

while in areas with moisture 

above field capacity, a more 

permeable metalized film was 

equally as effective at reducing 

emissions. Their studies confirmed that good agricultural 

practices are critical factors 

in determining how much fumigant is 

released into the atmosphere. The EPA 

has used the results, published in the 

journal Atmospheric Environment, along 

with results from other recent research, to 

develop the fumigant standards currently 

being considered.

Testing Film Quality

ARS researcher Sharon Papiernik and 

her colleagues used specially designed 

chambers to test the permeability of dozens 

of films used in field trials to come up with 

a “resistance factor” that measures each 

film’s ability to serve as a fumigant barrier. 

Papiernik sandwiched each film between 

two chambers, injected fumigants into one 

chamber, and measured both the fumigant 

that passed through the film into the second 

(receiving) chamber and fumigant that 

remained in the source chamber. Because 

each fumigant had a different chemistry, 

each behaved differently with each tarp.

The researchers tested 200 film-chemical combinations, including those used in 

large-scale field trials from the areawide 

pest management project, and came up 

with a resistance factor that can be used 

to determine emission rates for each 

film and fumigant under a wide range of 

growing conditions and weather patterns. 

Papiernik is research leader of the North 

Central Agricultural Research Laboratory 

in Brookings, South Dakota.

The results, reported online last year 

in the Journal of Environmental Quality, showed that the VIFs were in fact 

significantly better barriers to fumigant 

diffusion than the polyethylene films, but 

range from the chemistry of the fumigant 

to the temperature and the amount of water 

vapor in the air.

Such constantly shifting variables make 

it difficult to determine not only the amount 

of fumigant being released, but also its 

effectiveness at killing pests.

Researchers also need to determine how 

emissions rates are affected by a complicated list of crop-management decisions, 

such as the permeability of the film being 

used, the amount of time the film covers the 

fumigated soil, and the depth of the shank 

used to inject the treatment into the soil.

Scott Yates, research leader of the Contaminant Fate and Transport Unit at the U.S. 

Salinity Lab in Riverside, California, took a 

mathematical approach to the problem and 

developed a model focused on determining fumigant volatilization 

rates, the amount of fumigant retained in the soil, the 

amount released into the air, 

and the relationship between 

soil-chemical properties and 

emissions.

In work published in the 

Journal of Environmental 

Quality, Yates used the model 

to calculate fumigant emission 

rates that compared reasonably well to actual methyl 

bromide emissions observed 

in field trials where a polyethylene film was used to cover 

an 8-acre field. The model can 

be used to determine how a 

fumigant will be distributed throughout 

a field and offers a consistent method for 

determining emission rates under a wide 

variety of crop-management scenarios.—

By Dennis O’Brien, ARS.

This research supports the USDA priority of responding to climate change and 

is part of Methyl Bromide Alternatives 

(#308) and Air Quality (#203), two ARS 

national programs described at www.nps.

ars.usda.gov.

To reach scientists mentioned in this story, contact Dennis O’Brien, USDAARS Information Staff, 5601 

Sunnyside Ave., Beltsville, 

MD 20705-5129; (301) 

504-1624, dennis.obrien@ars.usda.gov.*

SCOTT YATES (D2248-2)

At an experimental site near Bakersfield, California, a tractor injects 

fumigants 46 centimeters deep into the soil while technician Qiaoping 

Zhang walks along the field and places boundary markers to identify the 

area of treated soil. Gas samples will be taken to determine fumigant 

emission rates in the field.

their effectiveness varied depending on 

the fumigant tested. Some VIFs were less 

effective under higher humidity levels. 

The EPA is developing this approach as 

the standard testing method for evaluating 

agricultural plastics used in soil fumigation. The results, along with those from 

other studies, have provided basic standards for film manufacturers and guidance 

for growers on which films offer the best 

options for reducing fumigant emissions.

Math Makes It Simple

A major goal in many fumigant studies 

is determining the amount of gas released 

from the soil during the fumigation period. 

But measuring and calculating emissions 

is no easy task. It means trying to estimate 

how much of a fumigant is released in an 

outdoor environment, where variables 
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 63

Decades of plowing throughout the 

Piedmont region of the United States have 

degraded the soil, allowing much of it to 

be washed away and robbing what is left 

of nutrients and organic matter. Sorghum, 

cotton, soybean, and wheat are still widely 

grown in the region, which stretches all 

the way from Alabama to New Jersey. But 

because the soil is so degraded, growers 

have allowed much of the land to revert 

to forests and pastures.

“Growers need guidance on whether 

keeping the land unused is the best way to 

restore degraded soils or whether allowing 

cattle to graze on it is a viable option,” 

says Alan Franzluebbers, an Agricultural 

Research Service ecologist at the J. Phil 

Campbell, Sr., Natural Resource Conservation Center in Watkinsville, Georgia. The 

center was started in 1937 to look for ways 

of improving soil quality for farmers in the 

southeastern United States.

Franzluebbers led a project where researchers planted grasses on 37 acres of 

rolling, eroded land in northeastern Georgia and allowed beef cattle to graze there 

to assess the effects on soil quality. Coastal 

bermudagrass was planted initially, and 

after 5 years, tall fescue was drilled into it, 

when the bermudagrass was in a dormant 

winter stage, to extend the grazing season 

from 5 months to 10 months of the year.

The research team, which included 

retired ARS scientists John Stuedemann 

and Stan Wilkinson, varied the number 

of cattle per acre, and over 12 years they 

assessed how the soils would respond to 

four different scenarios: moderate grazing 

(average of 23 steers for every 10 acres), 

intensive or heavy grazing (35 steers per 

10 acres), no grazing and letting the grass 

grow, and no grazing but cutting the grass 

for hay. Under each scenario they looked 

at the amount of soil compaction that occurred, the amounts of soil organic carbon 

and nitrogen found in the soils, and the 

amounts of surface plant residues, which 

help prevent erosion. Soil compaction 

makes it harder to grow crops. They also 

looked at the effects on the soil of three 

different fertilizer treatments (inorganic 

fertilizer alone, organic broiler litter alone, 

and a mix of inorganic fertilizer and organic 

broiler litter).

The team found that fertilizer type made 

little difference, but different grazing 

scenarios produced dramatically different 

effects. Land that was grazed produced 

more grass than ungrazed land, and grazing 

led to the most carbon and nitrogen being 

sequestered in soil. Sequestering carbon 

and nitrogen in the soil has become a major goal for agriculture because it reduces 

greenhouse gas emissions. Whether grass 

was grazed moderately or intensely made 

little difference on sequestration rates.

Cutting grass for hay reduced the amount 

of surface residue and increased soil compaction but didn’t change the amounts of 

organic carbon and nitrogen in the soil. 

Land left unused had the highest surface 

residue and least soil compaction and was 

better at sequestering carbon in the soil 

than haying.

From an environmental standpoint, 

grazing has traditionally been viewed 

as less desirable than leaving the land 

unused. But the results, published in the 

Soil Science Society of America Journal,

demonstrate that if growers manage cattle 

so that pastures are grazed moderately, 

they’re restoring soil quality and cutting 

greenhouse gases by keeping carbon in the 

soil as organic matter rather than releasing 

it into the atmosphere as carbon dioxide.—

By Dennis O’Brien, ARS.

This research is part of Climate 

Change, Soils, and Emissions, an ARS 

national program (#212) described at 

www.nps.ars.usda.gov.

Alan Franzluebbers is with the J. Phil 

Campbell, Sr., Natural Resource Conservation Center, 1420 Experiment Station Rd., 

Watkinsville, GA 30677; (706) 769-5631 

ext. 223, alan.franzluebbers@ars.usda.

gov.*

At an experimental field site in Oconee County, Georgia, technician Steven Knapp cuts a test 

plot to determine hay yield.

kim Lyness (D2136-1)

Cattle Pastures May 

Improve Soil Quality
64 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Red imported fire ants first arrived in the 

United States in the early 1930s and have 

been expanding along the southern portion 

of the country ever since. These ants inhabit 

more than 350 million acres in 12 southern 

states and Puerto Rico, and they have recently become established in isolated sites 

in California and New Mexico. For more 

than a decade, ARS scientists have gone 

on the offensive against red imported fire 

ants by using natural enemies against them.

Entomologist Sanford Porter has worked 

to collect, breed, and release phorid flies 

that are now used to control fire ant 

populations in the southern regions of 

the United States. Porter is at the Center 

for Medical, Agricultural, and Veterinary 

Entomology’s (CMAVE) Imported Fire 

Ant and Household Insects Research Unit, 

in Gainesville, Florida.

The fire ants’ large numbers and potent 

sting have resulted in medical, agricultural, 

and environmental economic impacts that 

cost the U.S. public billions of dollars each 

year. Scientists at CMAVE and cooperators 

in several states conducted a program to 

suppress fire ants in large areas. The areawide project involved cooperators in five 

states and was successful in establishing 

self-sustaining and spreading populations 

of phorid flies from South America.

The fire ant biocontrol program, which 

began in 1995, has released five species of 

phorid flies to parasitize the various sizes of 

fire ants—from the large to the very small. 

“The relationship between phorid fly and 

fire ant is very specific: The introduced 

phorid fly species only attack imported 

fire ant species,” says Porter.

After several years of testing, Pseudacteon cultellatus was recently approved for 

field release. This new species of phorid 

fly is currently being released at several 

sites in Florida to control tiny fire ant 

workers that belong to multiple-queen 

colonies. “These colonies are particularly 

problematic, because they usually house 

two to three times the number of worker 

ants,” says Porter. “Target release sites 

typically have a large number of fire ants, 

diverse plant life, and water nearby.

New Red Imported Fire Ant Enemies 

in Place for Fight

“Of the four phorid fly species previously 

released, only one has failed to establish 

itself and widely spread out. P. litoralis,

released in 2004 and 2005, was able to 

establish only in Alabama,” says Porter. 

“The others—P. tricuspis, P. curvatus, and 

P. obtusus—have expanded well beyond 

their release sites and are attacking fire 

ants in large regions. P. tricuspis and P. 

curvatus each cover about half of the U.S. 

fire ant range and are expected to increase 

to well over two-thirds of the range by the 

end of 2011.”—By Sharon Durham, ARS.

This research is part of Veterinary, Medical, and Urban Entomology, an ARS national 

program (#104) described at www.nps.ars.

usda.gov.

Sanford Porter is in the USDA-ARS 

Imported Fire Ant and Household Insects 

Research Unit, Center for Medical, Agricultural, and Veterinary Entomology, 1600-1700 

S.W. 23rd Dr., Gainesville, FL 32608; (352) 

374-5914, sanford.porter@ars.usda.gov.*

Entomologist Sanford Porter prepares to release several hundred fire ant workers parasitized by a 

new phorid fly species (Pseudacteon cultellatus) that prefers to attack the smallest fire ant workers.

Below: A phorid fly (left), Pseudacteon 

cultellatus, about 1 mm long, and a red 

imported fire ant (right), Solenopsis invicta, 

about 3 mm long. The fly can lay eggs inside 

the ant’s head. Fly maggots that hatch will then 

slowly decapitate the ant.

SANFORD PORTER (D2023-1)

PEGGY GREB (D2021-1)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 65

Sweetpotatoes earned U.S. producers about $395 million in 

2008—and they’re packed with carotenoids, vitamin C, potassium, and fiber. Now Agricultural Research Service (ARS) 

scientists have found that they also contain high levels of protective phenolic compounds called “caffeoylquinic acids.” These 

compounds, which are known for their antioxidant activity, are 

found in many plants, though the levels vary widely.

ARS agronomist Howard Harrison teamed up with plant 

pathologist Pat Wechter and plant physiologist Joseph Peterson 

(now retired) to measure the levels of caffeoylquinic acids in 

sweetpotatoes. All three scientists work at the U.S. Vegetable 

Laboratory in Charleston, South Carolina. Other ARS collaborators included ARS chemists Maurice Snook and Trevor Mitchell, 

who work at the Richard B. Russell Research Center Toxicology 

and Mycotoxin Research Unit in Athens, Georgia.

The scientists assessed the levels of four types of caffeoylquinic acids in 16 sweetpotato varieties from the United States, Brazil, 

and Africa. They also studied caffeoylquinic acids in bigroot 

morningglory, a sweetpotato relative with roots that can weigh 

more than 60 pounds.

The research team found measurable amounts of all four types 

of caffeoylquinic acids in the sweetpotatoes they tested. On average, the highest levels of the compounds were found in the layer 

of tissue just under the skin. Intermediate levels were found in 

the stele—the interior of the sweetpotato—and the lowest levels 

were found in the skin. Bigroot morningglory roots also had high 

levels of all four of the defensive compounds.

The scientists found that three of the compounds they tested 

provided some protection against Rhizopus soft rot, a fungus 

that infects sweetpotatoes after harvest by invading through 

breaks in the skin. All of the compounds inhibited growth of 

plant-infecting bacteria, and one inhibited another infectious 

plant fungus, Fusarium solani.

The team noted that the compound levels varied significantly 

among the sweetpotato varieties they evaluated, despite the 

study’s small sample size. “If we screened a larger sweetpotato 

germplasm collection, we’d probably find varieties with even 

higher compound levels,” Harrison says. He thinks that plant 

breeders may be able to use the compounds as biochemical 

markers to develop sweetpotato varieties with enhanced pest 

resistance and other beneficial traits.—By Ann Perry, ARS.

Howard Harrison is in the USDA-ARS U.S. Vegetable Laboratory, 2700 Savannah Hwy., Charleston, SC 29414; phone 

(843) 402-5300 ext. 5323, fax (843) 573-4715, e-mail howard.

harrison@ars.usda.gov. X

Sweetpotatoes Pack Potent Protection

Agricultural Research Service scientists Kurt Lawrence, 

Bosoon Park, Bob Windham, and Seung-Chul Yoon—all in 

the Quality and Safety Assessment Research Unit in Athens, 

Georgia—have made two improvements to a hyperspectral imaging system used to scan the surface of poultry carcasses for 

contaminants. They have refined the system 

so that it can detect even tiny amounts of 

fecal contamination, which can vary significantly depending on where in the digestive 

tract it originated. They have also developed 

and implemented a new image-processing 

method to identify and remove false-positive 

readings.

To facilitate the transfer of their system, 

a prototype on-line multispectral imaging system was installed 

and tested in a commercial poultry plant to detect fecalcontaminated carcasses. The system was developed through a 

research agreement with Stork Gamco, a manufacturer of poultryprocessing equipment based in Gainesville, Georgia. Carcasses 

were imaged after evisceration but before washing, at a rate of 

150 birds per minute. 

“The system ran for several days with no hardware or software 

problems, and it demonstrated the feasibility of accurately detecting fecal-contaminated carcasses,” says Lawrence.

The Athens team is collaborating with agricultural engineer 

Kevin Chao and biophysical scientist Moon Kim at the Beltsville Agricultural Research Center’s Environmental Microbial 

and Food Safety Laboratory, who developed an on-line imaging 

system to differentiate systemically diseased poultry carcasses 

from wholesome ones. 

The ARS groups and their industry partner are now merging 

the fecal-detection and diseased-carcass-detection systems onto a 

common platform that includes a line-scan hyperspectral imaging 

camera, lighting, and operating and detection software. Merging 

the two systems will aid in commercialization by creating 

one interchangeable imaging system that can be installed in 

different locations of the processing line to solve two separate 

and significant problems in the poultry processing industry. This 

will allow processors to more easily integrate such a system into 

their operations.

“We are currently modifying our system to work on the camera 

system used by the Beltsville group,” says Lawrence. “Our goal 

is to have the new prototype tested by the end of 2009.”—By 

Sharon Durham, ARS.

Kurt Lawrence is in the USDA-ARS Quality and Safety Assessment Research Unit, Richard B. Russell Research Center, 950 

College Station Road, Athens, GA 30605; phone (706) 546-3527, 

fax (706) 546-3607, e-mail kurt.lawrence@ars.usda.gov. X

“Seeing” Poultry Carcass Contamination

Science Update Science Update
66 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

A new technology that grades peanuts faster and more accurately is 

being researched by Agricultural Research Service scientists at the ARS 

National Peanut Research Laboratory 

in Dawson, Georgia. 

“The U.S. peanut industry is in a period of rapid economic and technical 

change, and this technology will help 

the industry maintain a competitive 

edge,” says Marshall Lamb, research 

leader at the lab.

Lamb was approached by peanut-industry representatives 

for help in solving labor-shortage issues by automating peanut 

grading. Engineer Hank Sheppard tested x-ray technology to 

determine whether such a system could handle the job. When 

compared to official peanut-grading methods, the technology 

delivered a 98- to 99-percent accuracy rate, and it was faster—7 

minutes versus 20 minutes per peanut grade sample.

“Official grading is labor intensive, requiring three to six 

people to hand-shell, pick, sort, and grade each nut,” says Sheppard. “The industry is having difficulty finding enough people 

to fill the worker requirements and who are willing to set aside 

3 months of the year to do this difficult job.”

Accordingly, the industry recently launched an initiative to 

improve current procedures or develop new technologies that 

would make peanut grading more efficient while ensuring—or 

even improving—accuracy and quality.

Another processing problem being addressed by ARS research 

is peanut moisture. Nuts must have a moisture content of 10 

percent or less to be suitable for further processing and shelling. 

The ability to determine moisture before grading begins would 

allow processors to divert high-moisture nuts for further drying 

instead of discarding them. Currently, the nuts are shelled, and 

then the moisture content is determined.

Chari Kandala, an agricultural engineer at the lab, has developed an automated in-shell moisture-detection system that could 

work in tandem with the x-ray grading unit to provide peanut 

processors a more efficient operation.

“We strive to help the peanut industry tackle important technical and quality issues. Applying these technologies may play a 

role in solving some of their problems,” says Lamb.—By Sharon 

Durham, ARS.

Marshall Lamb, Hank Sheppard, and Chari Kandala are with 

the USDA-ARS National Peanut Research Laboratory, 1011 

Forrester Dr., S.E., Dawson, GA 39842; phone (229) 995-7400, 

fax (229) 995-7416, e-mail marshall.lamb@ars.usda.gov, hank.

sheppard@ars.usda.gov, chari.kandala@ars.usda.gov. X

Helping the Peanut Industry

JACK DYKINGA (K4297-14)

Listeria monocytogenes—a foodborne pathogen—has been 

found in some ready-to-eat meats. It causes serious illness in 

about 2,500 people each year, resulting in 500 deaths. 

Though L. monocytogenes is killed by cooking or 

pasteurization, it can survive many chemicals used in in-plant 

sanitation programs. Thus, food can be contaminated during 

or after processing. The pathogen’s ability to grow at low 

temperatures may allow its growth in or on raw or improperly 

processed ready-to-eat foods even when they are refrigerated.

One source of contamination is work surfaces of processing 

plants where meat products are made. ARS microbiologist Judy 

Arnold at the Poultry Microbiological Safety Research Unit in 

Athens, Georgia, has been looking for improved methods to control biofilms containing L. monocytogenes. Any method needs 

to be acceptable to the U.S. Environmental Protection Agency.

Biofilms are protective layers of proteins and polysaccharides 

that surround bacteria and stick to equipment surfaces. “These 

protective shields trap spoilage bacteria and other pathogens that 

contaminate food during processing, and they resist cleaning 

and sanitizing,” says Arnold. “Today’s longer production runs 

provide more opportunity for biofilms to establish themselves, 

and today’s longer shelf life adds to the risk of biological 

contamination.”

In collaboration with Sterilex Corporation of Owings Mills, 

Maryland, Arnold has tested a proprietary formulation—based 

on alkaline peroxide and phase-transfer chemistry—that appears to be a cost-effective disinfectant for use in environments 

for poultry and meat production and processing. The formulation uses multiple chemical and physical actions to penetrate a 

biofilm, kill the microorganisms, and remove the biofilm from 

surfaces. It was tested against multiple disinfectants for killing 

and removal of L. monocytogenes biofilm. 

“Results showed that the formulation was 100 percent effective, providing total kill and more than 90 percent 

biofilm removal,” says Arnold. “This disinfectant is more effective than currently used 

disinfectants in reducing L. monocytogenes

biofilm growth, thus minimizing the risk of 

pathogenic contamination. Test evaluations 

also resulted in instructions for use that will 

meet USDA ‘zero tolerance’ regulations for 

L. monocytogenes.”—By Sharon Durham,

ARS.

Judy Arnold is in the USDA-ARS Poultry 

Microbiological Safety Research Unit, Richard B. Russell Research Center, 950 College 

Station Rd., Athens, GA 30605; phone (706) 

546-3515, fax (706) 546-3068, e-mail judy.

arnold@ars.usda.gov. X

Biofilms Have a New Foil

Science Update Science Update
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 67

Fungi May Hold Key to Reducing Grapefruit 

Juice Interactions with Medications

Grapefruit juice can interfere with 

the effectiveness of some medications 

because it contains furanocomarins, 

which are one of many types of 

phytochemicals commonly found in 

plants. Furanocomarins inhibit the 

enzymatic activities responsible for 

metabolizing certain medications 

and facilitating their release into the 

bloodstream. 

Researchers 

have found 

that the 

fungus 

Aspergillus 

niger 

either binds 

with grapefruit 

furanocomarins or enzymatically 

breaks them down. Studies are 

continuing to identify the enzymes in 

A. niger that prompt the breakdown 

of furanocomarins to see if these 

enzymes could be used to eliminate the 

compounds from grapefruit juice. 

In another study, when edible mushrooms that are related to A. niger—including morels and oyster and button 

mushrooms—were dried, pulverized, 

and added to grapefruit juice, they also 

removed furanocomarins. These findings provide additional evidence that 

proteins from A. niger and other fungi 

might someday lead to new methods 

for removing furanocomarins from 

grapefruit juice. Jan Narciso, USDAARS Citrus and Subtropical Products 

Laboratory, Winter Haven, Florida; 

(863) 293-4133, ext. 119, jan.narciso@

ars.usda.gov.

Food “Tattoos”: An Alternative to Labels for 

Identifying Fruit

Technology called “laser etching,” developed in part by ARS researchers, uses 

lasers to “tattoo” produce and could someday replace current labeling practices. A 

carbon dioxide laser beam is used to etch 

information into the first few outer cells 

of the peel on grapefruit, creating a mark 

that can’t be peeled off, washed off, or 

altered in any way. 

The tiny holes etched into the grapefruit 

peel are effectively sealed by the carbon 

dioxide, which prevents decay and entry 

by pathogens, but a coating of wax can 

further protect against water loss and 

pathogen entry. The original testing was 

conducted on grapefruit and has now been 

extended to include other citrus fruits, 

tomatoes, and avocados. The U.S. Food 

and Drug Administration is currently 

reviewing its application for commercial 

use. Jan Narciso, Citrus and Subtropical 

Products Research Laboratory, Winter 

Haven, FL 33881; (863) 293-4133 ext. 

119, jan.narciso@ars.usda.gov.

It Pays To Furrow Dike

Farmers who use furrow diking in their 

fields plow soils into ridge-like barriers 

that run alongside row crops. The ridges 

hold water and allow it to soak into the 

soil instead of washing away. Researchers 

compared the effects on runoff and erosion 

in southeast U.S. cotton fields with and 

without furrow diking. They found that 

furrow diking during a moderate drought 

saved farmers 1 inch of irrigation water 

per acre, reduced runoff by 28 percent, 

and curbed soil erosion. 

The following year, when drought conditions were more severe, it saved 5 inches 

of irrigation water per acre. The scientists 

also compared crop yields, water needs, 

and the effects of different irrigation rates 

between tracts of furrow-diked cotton and 

traditionally tilled cotton. Results indicated that in 1 of 3 years, cotton yield and net 

return were higher with furrow diking over 

four irrigation regimes, including dryland. 

Russell C. Nuti, National Peanut Research 

Laboratory, Dawson, GA 39842; (229) 

995-7449, russell.nuti@ars.usda.gov. 

Clinton C. Truman, Southeast Watershed 

Research Unit, Tifton, GA 31793; (229) 

386-7174, clint.truman@ars.usda.gov.

Science Update Science Update
68 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

First Hard Winter Wheat Varieties for 

Eastern U.S. Production

The first hard winter wheat varieties 

bred for production in the eastern United 

States have been developed by the Agricultural Research Service. 

Hard wheat, which is used for baking 

bread, has been a production challenge 

for farmers in the eastern United States 

because the area’s humidity increases 

the incidence of disease in the field, 

which affects yield and grain quality. But 

NuEast, a new variety of hard red winter 

wheat, has good grain yield and moderate 

resistance to powdery mildew and stem 

rust, including Ug99 races. It also has 

good resistance to leaf rust. 

Another new wheat variety on deck is a 

hard white winter wheat called “Appalachian White.” This variety was tested for 

3 years at six locations and consistently 

produced good yields and better grain 

quality than other hard white winter 

wheats tested. Appalachian White also 

showed a higher level of resistance to 

powdery mildew, stripe rust, leaf rust, 

and Hessian fly than other hard white 

wheats. David Marshall, USDA-ARS 

Plant Science Research Unit, Raleigh, 

NC; (919) 515-6819, david.marshall@

ars.usda.gov.

Roasting Does More Than Enhance Flavor 

in Peanuts

Researchers have shown that increasing 

roast color intensity steadily ramps up the 

antioxidant capacities of peanuts, peanut 

flour, and peanut skins. 

Peanuts were incrementally roasted 

at 362 ̊F from zero to 77 minutes and 

then sampled for water- and oil-soluble 

antioxidant activity levels. Dark-roasting 

consistently increased water- and oilsoluble antioxidant capacities for both 

commercially available peanut flours and 

blanched peanuts. Peanut skins, currently 

considered a waste product of industrial 

peanut processing, had remarkably high 

antioxidant capacities across all roast 

conditions. Antioxidant increases upon 

roasting in blanched seed peanut were 

attributed to greater concentrations of 

phenolic compounds and/or “browning” 

reaction products. 

The researchers also found that vitamin E degradation was most rapid in oil 

obtained from lightly roasted peanuts and 

that oil from darker roasted peanuts had 

better vitamin E retention than oil from 

lightly roasted or even raw peanuts. These 

findings could be a result of increased 

concentrations of oil-soluble Maillard 

reaction products, which seem to protect 

vitamin E from oxidation. Jack Davis, 

USDA-ARS Market Quality and Handling 

Research Unit, Raleigh, NC; (919) 515-

6312, jack.davis@ars.usda.gov.

Water Hardness Plays a Role in Removing 

Bacteria from Chicken Skin 

Water used in commercial poultryprocessing facilities can play a major 

role in the quality of the meat produced. 

Researchers have found that soft water is 

more effective than hard water in removing bacteria from broiler chicken skin. 

Hard water has higher concentrations of 

dissolved minerals like calcium and magnesium, and water is softened by removing 

these minerals. 

Scientists compared how well very 

hard, moderately hard, and soft water 

rinsed away different bacteria—including Campylobacter, Staphylococcus, and 

Pseudomonas—from the skin of broiler 

chicken carcasses. They found that soft 

water removed up to 37 percent more 

bacteria than the other two water types. 

The effectiveness of sanitization procedures to remove microorganisms from 

carcasses during processing is affected by 

several water-quality variables, including 

pH, ammonia concentration, microbial 

contamination levels, and hardness. 

These findings suggest that poultry 

processors might want to more closely 

monitor water hardness and its impact 

on carcass processing. Arthur Hinton 

and Ronald Holser, USDA-ARS Richard 

B. Russell Agricultural Research Center, 

Athens GA 30605; (706) 546-3621 

[Hinton], (706) 546-3361 [Holser], 

arthur.hinton@ars.usda.gov, ronald.

holser@ars.usda.gov.

Science Update Science Update

ARS studies show that the antioxidant 

content of peanuts and their oil is affected 

by roasting length.

JACK DYKINGA (K4297-14)
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 69

2009 South Atlantic Area—ARS Award Winners

Area Senior Research Scientist

Bruce W. Wood 

Byron, Georgia

For excellence in pecan production/protection research and 

advancing mineral nutrition management of crops.

Area Early Career Research Scientist

Mary J. Pantin-Jackwood

Athens, Georgia

For demonstrating the critical role of domestic ducks in 

the control of avian influenza viruses and for characterizing and improving diagnostics of novel enteric viruses of 

poultry.
70 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Special Administrator’s Award

ARS H1N1 Influenza Virus Research Team

Erica Spackman

David Suarez

Athens, Georgia

For outstanding, rapid research support and technology 

development to assist USDA, cooperating agencies, and 

the U.S. pork industry in responding to the 2009 H1N1 

pandemic flu threat.

Technology Transfer Awards

Outstanding Efforts

Second Generation Treatment System for the 

Green and Profitable Management of Livestock 

Manure

Matias B. Vanotti

Ariel A. Szogi

Patrick G. Hunt

Florence, South Carolina

For development of a green and profitable manure

treatment technology.

NCSU-ARS-IMS Microwave Technology Team

Van-Den Truong

Raleigh, NC

For development and transfer of a novel continuous-flow 

microwave heating process for producing large containers 

of aseptic shelf-stable vegetable and fruit purées.

Rift Valley Fever Outbreak Early-Warning Team

Kenneth J. Linthicum 

Seth C. Britch

Gainesville, Florida

For outstanding effort and creativity in the development 

and transfer of Rift Valley fever outbreak early-warning 

system to protect global agriculture and public health.
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 71

2010 South Atlantic Area—ARS Award Winners

Area Senior Research Scientist

Thomas E. Carter, Jr.

Raleigh, NC

For pioneering research on genetic diversity in soybean 

breeding and for developing the first high-yielding droughttolerant soybean germplasm.

Area Early Career Research Scientist

Russell C. Nuti

Dawson, GA

For conceiving and conducting research and transferring it 

to applicable stakeholders in the peanut industry.
72 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Technology Transfer Awards

Superior Efforts

C. Corley Holbrook

Tifton, GA

For development and transfer of Tifguard, the first highyielding peanut cultivar with resistance to both the peanut 

root-knot nematode and the Tomato Spotted Wilt Virus. 

H1N1 Pandemic Influenza Veterinary Diagnostic 

Test Development Team

David Suarez

Erica Spackman

For rapid response to the H1N1 pandemic influenza by 

timely development and transfer of diagnostic tests for 

veterinary specimens.
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 73

2011 South Atlantic Area—ARS Award Winners

Area Senior Research Scientist

Bosoon Park

Athens, GA

For pioneering research in hyperspectral and real-time 

multispectral imaging, and nanotechnology for food safety.

Area Early Career Research Scientist

B. Todd Campbell

Florence, SC

For innovative crop science research advances combining 

genomics and plant breeding.
74 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Technology Transfer Awards

Superior Efforts

Wheat Improvement Team

David Marshall

Myron Fountain

Lynda Whitcher

Charlie Glover

Raleigh, NC

Bill Brown

North Carolina State University

Raleigh, NC

For the development, release, and adoption of specialty 

wheat varieties for farmers, millers, and bakers, and for 

organic local foods in North Carolina.

Sustained Effort Technology Transfer 

Awards

Outstanding Efforts

Canal Point Sugarcane Variety Selection Team

Jack Comstock

Serge Edmé 

Barry Glaz 

Neil C. Glynn

Duli Zhao 

Jimmy D. Miller (retired)

Peter Y.P. Tai (deceased)

Canal Point, FL

For the sustained transfer of high-yielding CP sugarcane 

varieties to Florida, and internationally, and the transfer of 

variety selection procedures to Central America.

Adminstrator’s Outreach, Diversity, and 

Equal Opportunity Awards

Supervisory/Managerial Category

Bacterial Epidemiology and Antimicrobial 

Resistance Research Team

Mark Berrang

Paula Fedorka-Cray

Charlene Jackson

Jonathan Frye

Richard Meinersmann

Mark Englen

Athens, GA

In recognition of excellence in promoting diversity in ARS, 

mentoring students, and participating in student career and 

temporary employee programs.

AFM Support Award for Excellence

Bronze Award for Excellence

Nancy L. Sparks

Raleigh, NC

For leading users of the new financial system (FMMI) 

through the various processes, resulting in a better 

understanding of the system.
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 75

2009 South Atlantic Area—FLC 

Awards

FLC Award for Excellence in Technology 

Transfer

Kurt Lawrence

Bosoon Park

William Windham

Athens, GA

Kuanglin Chao

Moon Kim

Alan Lefcourt 

Beltsville Area

Beltsville, MD

Renfu Lu

Midwest Area 

East Lansing, MI

For hyperspectral imaging for food quality and safety 

inspection.

FLC Laboratory Director of the Year 

Patrick Hunt

Florence, SC

2010 South Atlantic Area—FLC 

Awards

FLC Laboratory Director of the Year

Kenneth Linthicum

Gainesville, FL

FLC Southeast Region Excellence in 

Technology Transfer–Honorable Mention

Corley Holbrook

Tifton, GA

For Tifguard, a peanut with resistance to both nematodes 

and viruses.

2011 South Atlantic Area—FLC 

Awards 

FLC Laboratory Director of the Year 

Patrick Hunt

Florence, SC
76 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

South Atlantic Area Contacts 

USDA, ARS, SAA 

Area Director's Office 

Richard B. Russell Agricultural Research Center

950 College Station Road 

Athens, GA 30605-2720 

Phone: (706) 546-3311 Fax: (706) 546-3398 

Deborah L. Brennan, Area Director (706) 546-3311 deborah.brennan@ars.usda.gov

Karl Narang, Associate Area Director (706) 546-3311 karl.narang@ars.usda.gov

Sharon Jett, Program Analyst (706) 546-3410 sharon.jett@ars.usda.gov

Armando Narvaez, Executive Assistant (706) 546-3328 armando.narvaez@ars.usda.gov

Melissa Harrell, Mgmt. & Program Assistant (706) 546-3078 melissa.harrell@ars.usda.gov

Jason Bray, Technology Transfer Assistant (706) 546-3496 jason.bray@ars.usda.gov

USDA, Agricultural Research Service (ARS) Website http://www.ars.usda.gov 

South Atlantic Area (SAA) Website 

http://www.ars.usda.gov/main/docs.htm?docid=6490

(on the website, click on the SAA location desired) 

South Atlantic Area 

Locations 

Athens, GA 

Charles Bacon, Research Leader and

 Location Coordinator

Toxicology and Mycotoxin Research Unit 

Richard B. Russell Research Center 

950 College Station Road 

Athens, GA 30605-2720 

Phone: (706) 546-3432, Fax: (706) 546-3116 

charles.bacon@ars.usda.gov

Richard Gast, Research Leader 

Egg Safety and Quality Research Unit 

950 College Station Road 

Athens, GA 30605-2720 

Phone: (706) 546-3445, Fax: (706) 546-3055 

richard.gast@ars.usda.gov

Arthur Vinton, Acting 

Research Leader 

Poultry Processing and 

 Swine Physiology Research Unit 

Richard B. Russell Research Center 

950 College Station Road 

Athens, GA 30605-2720 

Phone: (706) 546-3105, Fax: (706) 546-3633 

arthur.vinton@ars.usda.gov

Paula Cray, Research Leader 

Bacterial Epidemiology and 

Antimicrobial Resistance Research Unit 

Richard B. Russell Research Center 

950 College Station Road 

Athens, GA 30605-2720 

Phone: (706) 546-3305, Fax: (706) 546-3066 

paula.cray@ars.usda.gov
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 77

Kurt Lawrence, Research Leader 

Quality Assessment and Safety Research Unit 

Richard B. Russell Research Center 

950 College Station Road 

Athens, GA 30605-2720 

Phone: (706) 546-3497, Fax: (706) 546-3607 

kurt.lawrence@ars.usda.gov

Bruce Seal, Research Leader 

Poultry Microbiological Safety Research Unit 

Richard B. Russell Research Center 

950 College Station Road 

Athens, GA 30605-2720

Phone: (706) 546-3549, Fax: (706) 546-3771 

bruce.seal@ars.usda.gov

David Swayne, Laboratory Director 

Southeast Poultry Research Laboratory 

750 College Station Road 

Athens, GA 30605-2720 

Phone: (706) 546-3432, Fax: (706) 546-3161 

david.swayne@ars.usda.gov

Laszlo Zsak, Research Leader 

Enderruc Poultry Viral Diseases Research Unit 

Southeast Poultry Research Laboratory 

750 College Station Road 

Athens, GA 30605-2720 

Phone: (706) 546-3654, Fax: (706) 546-3161 

laszlo.zsak@ars.usda.gov

David Suarez, Research Leader 

Exotic and Emerging Avian Viral 

Diseases Research Unit 

Southeast Poultry Research Laboratory 

750 College Station Road 

Athens, GA 30605-2720 

Phone: (706) 546-3479, Fax: (706) 546-3161 

david.suarez@ars.usda.gov

Byron, GA 

Bruce Wood, Research Leader and

 Location Coordinator

Southeastern Fruit & Tree Nut Research Laboratory 

21 Dunbar Road 

Byron, GA 31008 

Phone: (478) 956-6420, Fax: (478) 956-2929 

bruce.wood@ars.usda.gov

Dawson, GA 

Marshall Lamb, Research Leader and

 Location Coordinator

National Peanut Research Laboratory 

1011 Forrester Dr., S.E. 

Dawson, GA 39842-0509 

Phone: (229) 995-7417, Fax: (229) 995-7416 

marshall.lamb@ars.usda.gov

Griffin, GA 

Gary Pederson, Research Leader and

Location Coordinator

Plant Genetic Resources Conservation 

Research Unit 

1109 Experiment Street, Redding Bldg. 160 

Griffin, GA 30223-1797 

Phone: (770) 228-7254, Fax: (770) 229-3323 

gary.pederson@ars.usda.gov

Tifton, GA 

Timothy Strickland, Research Leader and

Location Coordinator 

GA Coastal Plain Experiment Station 

P.O. Box 748 

Tifton, GA 31793 

Phone: (229) 386-3664, Fax: (229) 386-7215 

tim.strickland@ars.usda.gov

Corley Holbrook, Research Leader 

Crop Genetics and Breeding Research Unit 

GA Coastal Plain Experiment Station 

115 Coastal Way 

Tifton, GA 31793 

Phone: (229) 386-3176, Fax: (229) 391-3701 

corley.holbrook@ars.usda.gov
78 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

Brian Scully, Research Leader 

Crop Protection and Management Research Unit 

2747 David Road 

Tifton, GA 31793 

Phone: (229) 387-2330, Fax: (229) 387-2321 

brian.scully@ars.usda.gov

Charleston, SC 

Mark Farnham, Research Leader 

U.S. Vegetable Laboratory 

2700 Savannah Highway 

Charleston, SC 29414 

Phone: (843) 402-5301, Fax: (843) 573-4715 

richard.fery@ars.usda.gov

Clemson, SC 

Devron Thibodeaux, Research Leader 

Cotton Quality Research Station 

P.O. Box 792 

Clemson, SC 29633 

Phone: (864) 656-2512, Fax: (864) 656-1311 

devron.thibodeaux@ars.usda.gov 

Florence, SC 

Patrick Hunt, Research Leader 

Coastal Plains Soil, Water & Plant Research Center 

2611 West Lucas Street 

Florence, SC 29501-1241 

Phone: (843) 669-5203, ext. 101, Fax: (843) 669-6970 

patrick.hunt@ars.usda.gov

Raleigh, NC 

David Marshall, Research Leader and 

 Location Coordinator 

Plant Science Research Unit 

1419 Gardner Hall, NCSU 

Department of Plant Pathology 

Raleigh, NC 27695-7616 

Phone: (919) 515-6819, Fax: (919) 856-4816 

david.marshall@ars.usda.gov

Timothy Sanders, Research Leader 

Market Quality and Handling Research Unit

P.O. Box 7610, NCSU 

Raleigh, NC 27695-7610 

Phone: (919) 515-6312, Fax: (919) 513-8023 

tim.sanders@ars.usda.gov

Roger McFeeters, Research Leader 

Food Science Research Unit 

322 Schaub Hall 

Box 7624, NCSU 

Raleigh, NC 27695-7624 

Phone: (919) 515-2990, Fax: (919) 513-0180 

roger.mcfeeters@ars.usda.gov

Joseph Burton, Research Leader 

Soybean and Nitrogen Fixation Research Unit 

3127 Ligon St., NCSU 

Raleigh, NC 27607 

Phone: (919) 515-2734, Fax: (919) 856-4598 

joseph.burton@ars.usda.gov

Brooksville, FL 

Samuel Coleman, Research Leader 

Beef Cattle Research Unit 

Subtropical Agricultural Research Station 

22271 Chinsegut Hill Road 

Brooksville, FL 34601-4672 

Phone: (352) 796-3385, Fax: (352) 796-2930 

sam.coleman@ars.usda.gov

Canal Point, FL 

Jack Comstock, Research Leader 

Sugarcane Production Research Unit 

U.S. Sugarcane Field Station 

12990 U.S. Hwy. 441 

Canal Point, FL 33438 

Phone: (561) 924-5227, Fax: (561) 924-6109 

jack.comstock@ars.usda.gov 

Ft. Lauderdale, FL 

Ted Center, Research Leader 

Invasive Plant Research Unit

Invasive Plant Research Laboratory

3225 College Avenue 

Ft. Lauderdale, FL 33314 

Phone: (954) 475-6543, Fax: (954) 476-9169 

ted.center@ars.usda.gov 

Ft. Pierce, FL 

Calvin Arnold, Laboratory Director 

U.S. Horticultural Research Laboratory 

2001 South Rock Rd. 

Ft. Pierce, FL 34945 

Phone: (772) 462-5800, Fax: (772) 462-5900 

calvin.arnold@ars.usda.gov
Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights 79

Ed Stover, Research Leader 

Horticulture and Breeding Research Unit 

U.S. Horticultural Research Laboratory

2001 South Rock Road 

Ft. Pierce, FL 34945 

Phone: (772) 462-5836

ed.stover@ars.usda.gov

David Hall, Research Leader 

Subtropical Insects Research Unit 

U.S. Horticultural Research Laboratory 

2001 South Rock Road 

Ft. Pierce, FL 34945 

Phone: (772) 462-5897

david.hall@ars.usda.gov

Tim Gottwald, Research Leader 

Subtropical Plant Pathology Research Unit 

U.S. Horticultural Research Laboratory 

2001 South Rock Road 

Ft. Pierce, FL 34945 

Phone: (772) 462-5883 

tim.gottwald@ars.usda.gov

Gainesville, FL 

Kenneth Linthicum, Center Director 

Center for Medical, Agricultural &

 Veterinary Entomology (CMAVE)

1600/1700 SW 23rd Drive 

Gainesville, FL 32608 

Phone: (352) 374-5700, Fax: (352) 374-5852 

ken.linthicum@ars.usda.gov

Peter Teal, Research Leader 

Chemistry Research Unit, CMAVE 

1600/1700 SW 23rd Drive 

Gainesville, FL 32608 

Phone: (352) 374-5730, Fax: (352) 374-5707 

peter.teal@ars.usda.gov 

John Sivinski, Research Leader 

Insect Behavior and Biocontrol Research Unit, CMAVE 

1600/1700 SW 23rd Drive 

Gainesville, FL 32608 

Phone: (352) 374-5791, Fax: (352) 374-5804 

john.sivinski@ars.usda.gov

Robert Vander Meer, Research Leader 

Imported Fire Ant and Household Insects Research Unit, 

CMAVE 

1600/1700 SW 23rd Drive 

Gainesville, FL 32608 

Phone: (352) 374-5730, Fax: (352) 374-5818 

robert.vandermeer@ars.usda.gov

Gary Clark, Research Leader 

Mosquito and Fly Research Unit, CMAVE 

1600/1700 SW 23rd Drive 

Gainesville, FL 32608 

Phone: (352) 374-5910, Fax: (352) 374-5922 

gary.clark@ars.usda.gov

Miami, FL 

Robert Heath, Research Leader 

Subtropical Horticultural Research Unit 

Subtropical Horticulture Research Station 

13601 Old Cutler Road 

Miami, FL 33158 

Phone: (786) 412-3176, Fax: (305) 238-9330 

bob.heath@ars.usda.gov

Winter Haven, FL 

Elizabeth Baldwin, Research Leader 

Quality Improvement in Citrus and 

Subtropical Products Research Unit 

U.S. Citrus & Subtropical Products 

Research Laboratory 

600 Avenue S, NW 

Winter Haven, FL 33883 

Phone: (863) 293-4133 ext. 120, Fax: (863) 299-8678 

liz.baldwin@ars.usda.gov

Mayaguez, PR 

Ricardo Goenaga, Research Leader 

Tropical Crops and Germplasm Research Unit 

Tropical Agriculture Research Station 

2200 Pedro Albizu Capos Avenue, Suite 20 

Mayaguez, PR 00680 

Phone: (787) 831-3435 ext. 226, Fax: (787) 831-3386 

ricardo.goenaga@ars.usda.gov
80 Agricultural Research Reprint: South Atlantic Area Fiscal Year 2009-2011 Research Highlights

South Atlantic Area

Office of the Director

Deborah L. Brennan

Phone: (706) 546-3311

E-mail: deborah.brennan@ars.usda.gov

Web: www.saa.ars.usda.gov

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