Archives for category: Agriculture

Mycotoxins are small compounds found contaminating several plant products.  They are toxic to animals and humans in small doses and poisonings are often difficult to diagnose.  Symptoms of many mycotoxicoses are similar to each other and to those of other food poisonings and viral or bacterial diseases.

The story of aflatoxin, the first described mycotoxin, begins around 1960 in the United Kingdom.  A mysterious disease was running rampant through poultry farms, leaving upwards of 100,000 turkeys dead.  Veterinarians could not easily diagnose this new affliction labeled “Turkey X Disease”.  After ruling out known parasites, focus shifted to a common food source – a Brazilian peanut meal. The peanuts were found to be contaminated with a toxin they dubbed aflatoxin after the fungus found to produce it, Aspergillus flavus.

Aspergillus flavus fungus colonizing field corn (image: Maize Breeding Program at TAMU)

Aspergillus flavus fungus colonizing field corn (image: Maize Breeding Program at TAMU)

A. flavus colonizes oil-rich seeds, such as peanuts, maize (corn), cotton, ground nuts and pistachios.  Unlike many fungi, A. flavus and aflatoxin production are favored by hot and dry conditions.  In the United States, aflatoxin is a sporadic concern primarily for pets and livestock who consume corn and cottonseed products (See: 2006 and 2010 outbreaks in dry pet food).  However, it is a serious concern for human health in other parts of the world, most notably Kenya.  Highly toxigenic (produce high levels of aflatoxin) strains of A. flavus are native to regions in Kenya.  This combined with a maize-based diet and poor storage facilities (A. flavus can continue to grow and produce more aflatoxin after harvest if the grain is not kept dry) leads to aflatoxin poisonings every year in Kenya (even if they aren’t reported).  Aside from acute poisonings (involving liver failure and death), chronic exposure to aflatoxin can lead to liver cancer, jaundice, weight loss and immune system problems.  Aflatoxin can also pass from mother to baby through breast milk.  2004 marked the worst reported aflatoxicosis outbreak in Kenya and the world with 125 documented deaths.

A maize flour mill in Kenya (image: CDC).

A maize flour mill in Kenya (image: CDC).

What can be done?  Researchers have been focusing on understanding the populations of A. flavus in Kenya.  Atoxigenic (naturally produces no aflatoxin) strains of A. flavus have been identified and are being used as a biological control (A product called “aflasafe”) against more toxin strains.  The goal is for the toxin-free strains to outcompete the poison-producing ones in the maize fields, resulting in a less contaminated crop.  Extension and outreach programs have emphasized aflatoxin awareness for those who grow (management strategies, including the new bio control), store (keep it dry, inspect the grain) and sell maize (inspect before sale and production).

Please take a look at this slide show on aflatoxin management in Kenya.

Up next in this series, I’d like to discuss quantitative and qualitative testing methods for mycotoxins.  Testing is easier said than done (accurately), especially in a field setting.


Time to get back on track with our popular science updates.  These two stories peaked my interest this week:

Scientific American’s Agriculture and Innovation

This slide show gives us a peek at agricultural tools used 150 years ago when more than half of the U.S. population lived on a farm.  Some inventions border on absurd (like the combination sheep feeder and shearing table), while others are predecessors for modern tilling and harvesting machinery.  I think the drawings (all featured in issues of Scientific American from 1863) are works of art themselves.

Scientific American 1863 InnovationPhoto credit: Scientific American

Rare Flower Smells “like a dead rat in the wall”

Wait, this is news?  It is when the plant is rare and rarely flowers in nature, let alone in a cultivated setting (once every 7 to 10 years if you’re lucky).  The Amorphophallus titanum (The Titan Arum), commonly known as the corpse flower due to its unique fragrance, is part of the teaching collection at UC Santa Barbara.  This specimen, dubbed “Chanel”, bloomed July 31 and the sulfurous odor could be experienced throughout campus. The smell is attracts pollinators such as flies but a flower as rare as this attracted other guests of the human variety, as seen in this live feed.  To promote successful pollination, pollen was brought in from another A. titanum, which happened to flower the week prior at the U.S. Botanic Garden in Washington DC.  Good timing!

UCSB Titan AramPhoto Credit: Julie Cohen

PS – A video of a Titan Arum that bloomed in 2006 at the Brooklyn Botanic Garden, including time-lapse photography.

What have you been reading this week?


Welcome back to our Mycotoxin Series!

With wheat harvest mostly complete for the eastern United States, it only seems fitting that I write about deoxynivalenol (DON).  DON is produced by Fusarium graminearum (amongst others) and can be found in products made with wheat, barley and corn.  DON has been dubbed the “most commonly encountered” mycotoxin.  This is likely due to our diets (wheat and corn are staple crops in many cultures and are used in many food products) and much of the wheat we grow is rather susceptible to F. graminearum.

 FHB wheat head katelynwillyerd

F. graminearum is the causal agent of Fusarium head blight of small grains (also known as Scab).  The disease is characterized by premature “bleaching” of the wheat heads (see above), shriveled kernels, reduced yield and DON contamination.  F. graminearum also causes a disease in corn called Gibberella ear rot (more of a concern for livestock).  DON serves as a virulence factor for F. graminearum which means DON is a powerful “weapon” for this pathogen as it infects the plant.

DON is a mycotoxin that is harmful to both plants and animals (any eukaryotic cell, for that matter).  DON binds to ribosomes, preventing cells from translating genes to proteins (remember, Bio 101: DNA –> mRNA –> amino acids/proteins).  Without essential proteins, cells are unable to carryout basic function and die (e.g. bleached, dead tissue on wheat heads).

DON is also known as “vomitoxin”.  This gives you a pretty specific idea about what sort of symptoms we observe in humans and animals suffering from DON poisoning.  DON may also cause other gastro-intestinal distress, poor nutrient absorption, reduced weight gain, feed refusal and impaired immunity.  Despite being the most commonly encountered mycotoxin, we don’t have a good handle on the effects of chronic exposure to low doses of DON that may be in our breakfast cereals, breads, pretzels, pastas, etc.

DON facts katelynwillyerd

PS – A fact sheet I co-wrote on DON in corn in Ohio

Welcome back to our Mycotoxin Series!

Patulin wouldn’t be the first mycotoxin I’d typically introduce, but it has been in the news recently.  Patulin is produced by species of Penicillium, Aspergillus and Byssochlamys, which are filamentous fungi or “molds”.  Patulin can be found contaminating products like fruit, grains and cheese; however, apple juice is of most concern.  And let’s be real, it’s the bruised, damaged and misshapen apples that go into juice (blemish-free are reserved for fresh market’s picky consumers).  However, apples with rot (see below) should NOT go into juice or cider production due to patulin concerns.

apple with Penicillium expansum

Apple infested with Penicillium expansum, a patulin producer.
[NOTE: The blue-gray growth is the fungus. Patulin (waaaaay too small to be seen by the human eye!) is produced by the fungus and spreads into the rotten apple.]

Photo: Puel et al. 2010. Toxins (Basel). 2(4): 613–631.

In April 2013, Winn Dixie brand apple juice was voluntarily recalled due to patulin levels over 50 parts per billion (ppb).  In June 2013, researchers from the University of Granada reported that more than 50% of commercial apple juices tested contained >50 ppb patulin (50 ppb is the “limit” for patulin in both the US and EU).

Healthy apples

Healthy apples

Patulin in apple juice is of particular concern as this product is frequently served to young children.  In fact, some of the commercial juices tested in the aforementioned study were specifically produced and marketed to children. This toxin is a suspected carcinogen and symptoms of a patulin mycotoxicosis (poisoning) are gastro-intestinal inflammation and ulcers, weight loss, swelling, convulsions and impaired immune response (source).

While I’m not a medical doctor or veterinarian, eliminating the contaminated product from one’s diet often alleviates the symptoms.  However, acute mycotoxin poisonings are rare in the US (especially for humans).  Chronic exposure to low levels of mycotoxins is much more concerning and is difficult to study.  Hopefully, juice producers will step up their mycotoxin testing protocols to reduce the levels of patulin on the grocery shelves.

Optional subtitles: Why should I care? Do I really want to know? Thanks a lot Debbie Downer.

Consumers are becoming increasingly aware of and passionate about food quality and safety.  Not a day goes by that you don’t hear buzz words like “organic”, “GMO”, “hormone-free”, “free range”, etc.  Here in the United States, we have a (relatively) safe and secure supply of food.  However, when that security is compromised, it can be big news:

GMO wheat found in Oregon (2013)

Salmonella (2012) and Listeria (2011) found on cantaloupe

E. coli on salad greens in California (2006)

Over the next few weeks I’d like to talk about another threat that can also sicken humans and animals but doesn’t often receive a lot of press: Mycotoxins.  Mycotoxins are pervasive and fascinating, in my opinion.  However, I did spend much of PhD and post doc studying them…

What is a mycotoxin? “Myco” means fungus and a toxin is a poison; mycotoxins are small compounds produced by some fungi that are harmful to humans and animals in small doses. Symptoms of mycotoxin poisoning in humans and animals are known as mycotoxicoses. Mycotoxins associated with “poisonous mushrooms” are easy enough to avoid (don’t eat them!).  However, mycotoxins are frequently found contaminating food and feed products and are consumed unknowingly.


Many species of fungi that produce mycotoxins are also plant pathogens.  As part of their infection and colonization of the plant, they produce these toxins which end up in parts of the plant humans and animals eat. I’ll be profiling specific mycotoxins in the weeks ahead, but (spoiler alert!) some of the crops frequently contaminated with mycotoxins are wheat, corn and peanuts.

Interestingly, we don’t know why fungi produce these toxins.  Hypotheses include antiherbivory (protect a host plant and fungus from being eaten), defense against competitors (a weapon against other fungi or microbes), promotes virulence/aids in causing disease or performs some unknown function in fungal cells.

Stay tuned for more in the Mycotoxin Series.

PS – Fungi are really cool organisms and produce many compounds that have been beneficial for humans, such as dyes, penicillin, statins (for high cholesterol), etc!

The stories I’ve been reading…

But first a gratuitous wheat shot, because I can’t resist those amber waves of grain:


1. It was reported last week that Monsanto’s Roundup-ready (glyphosate-resistant) wheat was uncovered in Oregon.  The catch?  Monsanto field-tested the wheat nearly 10 years ago but never released it for commercial use.  Roundup-ready corn and soybeans, which are resistant to the herbicide glyphosate, are widely grown in the US. However, these crops are generally processed or used as animal feed, whereas wheat is consumed directly by humans. There is global alarm over genetically modified (GM) foods in our diets and prolonged exposure to these foreign genes. Monsanto dropped the GM wheat project over producers’ trade concerns. As a result of this finding in Oregon, Japan has suspended wheat imports from the Pacific Northwest. Japan is the top importer of US wheat. So far there is no evidence that GM wheat has entered the food supply, but one has wonder if the presence of GM wheat on one Oregon farm is a unique occurrence.

Update: Monsanto is being sued by farmers in the Pacific Northwest over loss of business due to the GM wheat scare.

2. Scientific American reports another contributing factor of honeybee colony collapse may be the alterations to domesticated honeybee diets.  Of course the natural food source of the honeybee is its honey, but when we harvest it for human use the bees are given sugary syrups instead.  Most researchers agree that pesticide use is the predominate cause of colony collapse, but poor nutrition certainly adds to the bees’ stress, I would think.

What have you been reading?

We eat a lot of potatoes in our house.  Having a vegetarian and meat-eater in the house can make mealtimes stressful, but baked potatoes topped with broccoli for me and bacon for him makes us both happy.  I kid, but in early nineteenth century Ireland potatoes were no joke… they were the staple food for the lower class, the landless laborers.

Existing dependent on a single food source is risky and in 1845 a plant disease epidemic took out the potato in Ireland (in the field and in storage).  The disease would later be named late blight and is regarded as the disease that birthed the study of plant pathology.   The causal agent of late blight is a Phytophthora infestans (Latin for “plant destroyer”), fungal-like organism called an oomycete.  As a result of this microscopic killer, an estimated 1 million Irish starved and another 1.5 million emigrated from Ireland, dramatically changing not only Ireland but countries like the United States that received the displaced.  Late blight remains a significant threat to potato and tomato industries today (2009 epidemic in Northeast US); however, we now have management options such as fungicides and moderately resistant varieties to minimize losses.

Potato with late blight (foreground); Potato treated with fungicides (background)

Potato with late blight (foreground); Potato treated with fungicides (background)

(Image: Courtesy D. Inglis via

Last week, Yoshida et al. (2013) released a study identifying the specific strain (or genotype) of P. infestans responsible for the Irish Potato Famine. Researchers isolated samples of the pathogen from preserved potato leaves with late blight symptoms and compared them to modern strains with DNA analysis.  Genotype HERB-1 was consistently isolated from the historic Irish samples, suggesting it was the strain responsible for the late blight epidemic.  HERB-1 is different from modern genotypes and is likely extinct, having been replaced by US-1 by the 20th century, as the predominate genotype outside of P. infestans center of origin (Mexico).  Researchers also note that while US-1 and HERB-1 are related, US-1 is not a direct ancestor of HERB-1.

I think one of the most interesting parts of this study was the use of preserved herbarium samples to generate the dataset.  Just think of other pathogen populations and histories that could be elucidated using this approach!  Aside from the cool factor, understanding how these pathogens evolve is vital for developing new management strategies.

 PS – For more on late blight click here.

Happy Friday!  Here are the stories I’ve been reading this week…

1. Amphibian plague

The fungus Batrachochytrium dendrobatidis (Bd, the chytrid fungus) is the causal agent of chytridiomycosis, a fatal disease of frogs.  In the May 2013 issue of EcoHealth, Grower et al. report that Bd can also infect and kill a limb-less, snake-like group of amphibians called caecilians in the wild.  Unless you’re an avid caecilian enthusiast (they’re out there), you may be wondering ‘so what’.  Adding more species to the Bd-susceptible list is notable because some researchers are hypothesizing that this fungus may cause disease in ALL amphibians.  Imagine a pathogen with the ability to infect all mammals.  The chytrid fungus has already been blamed for the extinction of nearly 300 amphibian species.  Furthermore, knowing Bd infects the soil-dwelling caecilian suggests that the pathogen is adept in soil survival.  It was previously known that Bd survives and is spread via water, thanks to its swimming zoospore.

caecilian, Natural History Museum via Natural History Museum via

2. Cal State leaning toward virtual labs?

Officials at the California State University system are trying to solve the problem of “bottleneck courses”; those that difficult for students to get into, thus slowing their advancement or even causing them to drop out.  Some of these identified courses are required lab-based science courses for non-majors.  One solution may be to enroll students in virtual lab classes, involving simulations of experiments.  On one hand, this alleviates the bottleneck issue while still providing students with exposure to basic theories, problem-solving, scientific method, etc.  However, as Cal State professor Jeffery Bell cautions, the virtual lab may be too abstract for some students and give them a false appreciation of what scientists really do.  I have to agree and I’d hate to see lab sections for non-majors completely eliminated in favor of simulations.  There’s a “cool” factor to science (preparing a specimen and observing it under a real microscope, for example), that doesn’t quite translate to viewing something on a computer.

3. The Case of the Irish Potato Famine

I’m planning to write more about the Irish Potato Famine next week since it’s one of the great historical plant pathology stories (yes, we have those).  While the causes of the Irish Potato Famine are political as well as biological, it was announced this week that the particular strain of Phytophthora infestans, the pathogen responsible for destroying millions of potatoes in 1840’s Ireland, has been genetically identified.  This strain, known as HERB-1, was responsible not only for the deaths of an estimated 1 million people but also immigration of many Irish to the United States and other parts of Europe.  More next week…

Honeybees play a crucial role in agriculture, and I’m not only referring to the honey that we use for baked goods and at tea time.  Sorry, Pooh Bear. Pollination of many fruit and vegetable crops is facilitated by honeybees when gathering nectar from flowers of these plants.  Only following successful pollination and fertilization of said flowers can fruits and vegetables begin to grow.  Therefore, bee population and health is directly tied to our supply of many fruits and vegetables you see in gardens, farmers markets and in grocery stores:

common crops pollinated by bees

In 2006, beekeepers and scientists became aware of a phenomenon in which honeybees appeared to abandon their hives.  In most cases, the queen was still alive and no dead bee bodies were found inside.  The name for this condition is just as mysterious: colony collapse disorder (CCD).  Prior to 2006, a beekeeper could expect to lose 1 out of 10 hives during typical winter.  Due to CCD, losses have tripled and could potentially reach 50%.

The cause(s) of CCD have not been proven, but may be related to pathogens, pests (Varroa mites are frequently associated with CCD), poor nutrition, mismanagement of hives, environmental stress (drought) and agricultural chemicals.  Recently, one class of insecticide has been “accused” of being the cause of CCD: neonicotinoids, which have been used since the 1990s on a wide variety of vegetable and field crops as a soil, seed or foliar treatment.  The evidence is mounting against neonicotinoids, causing the European Commission instituted a 2-year ban on these insecticides earlier this month.  However, many researchers are questioning the effectiveness of the ban as CCD is widely thought to have more than one causal agent.  More research is definitely required to alleviate bee shortages and secure the future of our favorite pollinators and crops.

PS – Penn State entomologists have been leading the way in pollinator research.  Talking CCD on BBC News Hour (go to 17:50).

Have you been tuning to Coffee Week on NPR’s Morning Edition this week?  They’ve highlighted coffee’s production, culture, politics, economics and more, and one particular piece, entitled “Exploring Coffee’s Past to Rescue Its Future” by Dan Charles, caught my attention as a plant pathologist.  You can listen to the story here or check out the written accompaniment here.  Charles highlights a challenge to coffee production: the lack of diversity in coffee varieties that are in production today. 

You see, the majority of coffee (Coffea arabica) grown all over the world originates from 2 genetic lines, Bourbon and Typica.  These lines were likely selected for their favorable agronomic qualities, such as yield, and characteristics desired/demanded by the consumer, such as taste or roasting properties.  However, due to a fungal plant disease called coffee rust, popular varieties of coffee may fall short; that is, they weren’t originally bred for resistance plant disease.  And since coffee essentially hails from the same genetic background (lack of diversity) and growers plant them throughout coffee growing regions, we’ve created the perfect storm where nearly all coffee is susceptible to coffee rust. Coffee rust damages the leaves and without leaves, the plant cannot produce quality berries.  No berries? No beans. No coffee.  Ok, “no coffee” may be a little dramatic, but coffee rust has the ability to increase production inputs, limit supply and eventually drive up the cost for your bag of beans.

 Coffee rust lesions. Image: P.A. Arneson via

Coffee rust lesions. Image: P.A. Arneson via

This challenge is not unique to coffee production and can be seen in nearly all crops grown by man, including staples such as rice, corn, wheat and potatoes.  As they mention in the piece, research centers to explore the genetics of these staple crops have been established throughout the world but not for coffee.  Studying and preserving diversity of domesticated plants is essential to combating plant disease and one of the best places to look for novel disease resistance genes is in the plant’s center of origin, where the plant is thought to have evolved.  The center of origin for coffee is Ethiopia and wild coffee and other species of Coffea collected there are being studied, cataloged and evaluated for resistance to coffee rust.  The goal is to incorporate the qualities demanded by consumers and growers with improved disease resistance.

Kinda makes you want to savor that morning cup of joe a little more, doesn’t it?  It’s one of those things I appreciate about agriculture and that’s something as simple as a coffee bean has a vast and complicated story; one than has woven itself deeply into cultures around the world.

 Historic Distribution of Coffea arabica.  Image: Specialty Coffee Association of America via

Historic Distribution of Coffea arabica.
Image: Specialty Coffee Association of America via

Image: Specialty Coffee Association of America via

PS – a coffee quiz

PPS – Coffee rust isn’t new.  It’s one of the reasons the British historically drink tea! Confused? Check this out!