Managing Diseases without Fungicides: A Focus on Sanitation (A Visiting Professor feature)

Submitted by:
Nicole Ward Gauthier,
University of Kentucky Extension Plant Pathologist
PEOPLE: University of Kentucky Department of Plant Pathology Website
Kentucky Diseases of Fruit Crops, Ornamentals, & Forest Trees on Facebook
Amanda Sears, Kentucky Extension Horticulture Agent
Madison County Cooperative Extension Website

Alternatives to Fungicides

When diseases occur in urban landscapes, it is often presumed that fungicides are the most important and effective disease management tools available. However, a good sanitation program can help reduce the need for chemical controls and can improve the effectiveness of other practices for managing disease. This often-overlooked disease management tool reduces pathogen numbers and eliminates infective propagules (inoculum such as fungal spores (figure 1c) , bacterial cells; virus particles; and nematode eggs) that cause disease.

fig 1b marigold botrytis 1525420 (MC Shurtleff, UIll bugwd) (640x412)
Figure 1a. Marigold blossom infected with Botrytis
  Figure 1b. Pathogen levels can build up on marigold flowers if diseased tissue is left in the landscape

Figure 1b. Pathogen levels can build up on marigold flowers if diseased tissue is left in the landscape
close up of infecting spores
Figure 1c. Infecting spores on plant surface

Certain foliar fungal and bacterial leaf spots can become prevalent during rainy or humid growing seasons. When disease management is neglected, pathogen populations build-up and continue to increase as long as there is susceptible plant tissue available for infection and disease development (Figures 1a-c). Infected plant tissue infested soil and pathogen inoculum all serve as sources of pathogens that can later infect healthy plants.

Figure 2. Fallen leaves can serve as a source of inoculum (fungal spores) for additional infections. Many pathogens overwinter in fallen debris and then produce infective spores the following spring.

Reduction of pathogens by various sanitation practices can reduce both active and dormant pathogens. While actively growing plants can provide host tissue for pathogen multiplication, dead plant material (foliage, stems, roots) can harbor overwintering propagules for months or years (Figure 2).

These propagules can travel via air/wind currents, stick to shoes or tools, or move with contaminated soil or water droplets. Thus, prevention of spread of pathogens to healthy plants and the elimination of any disease-causing organisms from one season to another are the foundations for a disease management program using sanitation practices.

Sanitation Practices

Elimination and/or reduction of pathogens from the landscape results in fewer pathogen propagules. The following sanitary practices can reduce amounts of infectious pathogens:

Figure 3a. Cankers are common overwintering sites for disease-causing pathogens
  • Remove diseased plant tissues from infected plants. Prune branches with cankers (Figure 3a) well below the point of infection (Figure 3b). Cuts should be made at an intersecting branch. Rake and remove fallen buds, flowers, twigs, leaves, and needles.
Figure 3b. Remove infected branches, making cuts well below points of infection
  • Disinfest tools used to prune galls and cankers.  Cutting blades should be dipped into a commercial sanitizer, 10% Lysol disinfectant, 10% bleach, or rubbing alcohol between each cut.
  • If using bleach, rinse and oil tools after completing work, to prevent corrosion.
  • Discard perennial and annual plants that are heavily infected and those with untreatable diseases (e.g. root rots, Figure 4; and vascular wilts).  Dig up infected plants to include as much of the root system as possible, along with infested soil.

infected plant                           imag

Figure 4. Heavily infected plants or those with untreatable diseases, such as black root rot (images left and right), should be removed from the landscape.   

  • Trees and shrubs infected with systemic diseases (e.g. Dutch elm disease, Verticillium wilt, bacterial leaf scorch) that show considerable dieback should be cut and the stump removed or destroyed (e.g. by grinding).
  • If infected plants are to be treated with fungicides, prune or remove infected tissue (flowers, leaves) and debris to eliminate sources for spore production or propagule multiplication.  This should be done before fungicide application. Fungicide effectiveness may be reduced when disease pressure is heavy, which can result when pathogen levels cannot be reduced sufficiently by chemical means (fungicides).
  • Discard fallen leaves, needles (Figure 5), prunings, and culled plants. Never leave diseased plant material in the landscape, as pathogens may continue to multiply by producing spores or other propagules.  Infected plant material should be buried, burned, or removed with other yard waste.

pathogen 1       pathogen 2

Figure 5.  Black fruiting structures of the pine needlecast pathogen contain spores (images left and right). Removal of infected plant tissue helps reduce amounts of inoculum in the landscape.

  • Do not compost diseased plant material or infested soil because incomplete composting (temperatures below 160˚ F) may result in survival of propagules.
  • Homeowners should be cautious about storing diseased limbs and trunks as firewood or using the woodchips as mulch.  For example, wood from trees infected with Dutch elm disease should be debarked before placing in a firewood pile.
  • Remove weeds and volunteer plants to prevent establishment of a “green bridge” between plants.  A green bridge allows pathogens to infect alternate hosts until a more suitable one becomes available.  Be sure to remove aboveground parts AND roots.
  • Soil from container-grown plants should not be reused from one season to the next because pathogens can survive in soil.

Additional Resources:

University of Kentucky Extension Plant Pathology Publications

Photo credits:

R.K. Jones, North Carolina State University (Fig. 1A), courtesy
M.C. Shurtleff, University of Illinois (Fig. 1B), courtesy
David Cappaert, Michigan State University (Fig. 1C), courtesy
Theodor D. Leininger, USDA Forest Service (Fig. 2), courtesy
Joseph O’Brien, USDA Forest Service (Fig. 3, right), courtesy
Elizabeth Bush, Virginia Tech (Fig. 4, left), courtesy
Bruce Watt, University of Maine (Fig. 4, right), courtesy
Andrej Kunca, National Forest Centre, Slovakia (Fig. 5, left), courtesy
Robert L. Anderson, USDA Forest Service (Fig. 5, right), courtesy
John R. Hartman, University of Kentucky (Fig. 3, left)

 pdf  Managing Diseases Without Fungicides

Organic insecticides that will get you high


Plants are crazy chemical factories, synthesizing a whole host of compounds that we use for flavoring and dye and medicine and… getting high. And why are they making all these chemicals? They’re certainly aren’t doing it for our sake… no, quite often they’re trying to kill something – usually insects — and it just so happens that sometimes our brains and bodies react differently enough that instead of killing us, they make us high. Well, and sometimes they kill us too.

Nicotine, the addictive force behind cigarettes, is a potent natural insecticide. if you’ve heard of neonicotinoids, the pesticides that some are concerned with in relation to honey bee health, they’re synthetic insectides based on the chemistry of nicotine, and like it, they effectively kill insects. No word on if anyone has tried smoking them yet.

Opium poppies are full of a thick latex loaded with chemicals like morphine and codeine, to name a few, which are obviously used as pain killers, and of course opium is taken directly or processed into more potent forms like heroin. The research on these chemicals indicates multiple possible functions, acting to prevent damage by herbivores (like insects), and possibly also acting to prevent pathogen damage and maybe even a more structural function in strengthening cell walls in response to damage  (see: I didn’t find any research looking directly at opium’s ability to kill insect pests. Probably because that type of research is usually aimed at a practical solution to pest problems, and even if heroin proves to be a potent insecticide, I doubt anyone would issue and extension bulletin recommending you use it to control your whitefly…

But that lack of practical application didn’t stop a researcher from publishing a paper titled  Cocaine as a Naturally Occurring Pesticide in which they found that cocaine was highly effective in killing tomato hornworm! Organic growers, take note! Maybe THAT’S why organic tomatoes are so expensive at the farmers market…

In any case, it is fascinating to note all the interesting, sometimes useful, often dangerous chemicals that have evolved thanks to the on-going chemical arms race between plants and the things that try to eat them. We’re the accidental beneficiaries – and sometimes victims – of that very, very old battle.

New publication on biodynamics

Happy New Year to our blog readers!

Now that we have our blog safely moved to this new format, we all resolve to post more frequently. (It’s actually Bert’s day to post, but given that his computer is probably frozen – literally – in Michigan, I’ll step in.)

Today I got a link to my most recent publication in HortTechnology on the science behind biodynamic preparations. I’ve written about this topic before, but recognize the importance of peer-reviewed information for researchers, extension educators, and Master Gardener volunteers. Not to mention all the gardeners who rely on us to provide good science for gardens and landscapes. So here it is. I’m planning to continue submitting review articles to HortTechnology on other topics of interest. It looks like permaculture might be the next one up.

So enjoy this article – pass it on to others who are curious about biodynamics, and if you are a Master Gardener be sure to take it to your MG coordinator and ask that it becomes a resource for your program.


Conventional vs. organic agriculture – the battle continues

An article was published earlier this week comparing the nutritional content of milk from organically raised cows to that from conventional dairies. The principle finding in this report is that “organic milk contained 25% less ω-6 fatty acids and 62% more ω-3 fatty acids than conventional milk, yielding a 2.5-fold higher ω-6/ω-3 ratio in conventional compared to organic milk (5.77 vs. 2.28).” (ω-3 fatty acids are considered to be “healthy” and you’ve probably heard of them in association with fish consumption.)

Of course, the popular press has had a field day with this, with such headlines as “Study finds organic milk is more nutritious.” This of course is nonsense, because the researchers didn’t study the health effects on people consuming the milk. But for argument’s sake, let’s assume this might be true and move on to the study itself.

What researchers actually found was that cows who feed primarily on pasture grasses and other forages (the “organic” cows) had elevated ω-3 fatty acids compared to those receiving a primarily grain-based diet (the “conventional” cows). This isn’t new information – other studies (such as this one) have consistently demonstrated this.

The problem with this newest paper is the inaccurate terminology used to describe the study. It really has nothing to do with whether the cows are raised organically or conventionally – it has to do with what they eat. A better experimental design would have included multiple comparisons among “organic” cows (who by default are grass-fed), “conventional” cows that are fed a grain diet (typical with large operations), and “conventional” cows that are pasture-raised (common with smaller farms that don’t want to jump through the organic certification hoops). I’m betting that the milk from this last group of cows wouldn’t be much different from the “organic” cows.

The upshot of using such imprecise terminology is that the message is lost amid the furor of the ongoing organic vs. conventional agriculture battle. Readers erroneously jump to a  value-based conclusion – i.e., organic is “better” than conventional.

In my opinion, there’s no excuse for this. The experts who reviewed this article should have pointed out the loaded language and insisted on a change in terminology. (You might be interested to follow the comments on this article, one of which alludes to misleading terminology.)

Why I Don’t Worry Too Much About Organic Fruits and Veggies

Let me tell you something you already know.  If you grow something in your own garden you’ll know exactly what poisons were or weren’t put on it, how much fertilizer was used, and furthermore it will taste better.

If you buy your apples from the guy down the street who you’ve known for 20 years you’ll be able to ask him what he used to grow the crop, why he used it, and you’ll have the satisfaction of supporting a local industry.  And yes, those apples will taste better than grocery store apples.

If you go to a farmers market you’ll be able to ask the people there exactly what they did to their crops, and why they did what they did.  And you’ll feel good about supporting the local economy.  And yes, the food will taste better than anything from the grocery store.

If you walk into a grocery store or Target, or Kmart or whatever and pull a fruit or vegetable off the shelf which has the USDA Organic Label on it and say to yourself “Hey, I’m doing something good for my family and the environment” then, in my opinion, you’re fooling yourself.

There, I said it.  I believe that, AS USDA ORGANIC CERTIFICATION NOW EXISTS, the USDA Certified Organic label does not provide a significant indicator that the fruit or veggies you’re buying provide a significant benefit in terms of human or environmental health.  Please note that I’m not saying anything different than our government does – what they say is: “Organic is a labeling term that indicates that the food or other agricultural product has been produced through approved methods that integrate cultural, biological, and mechanical practices that foster cycling of resources, promote ecological balance, and conserve biodiversity.”

Notice that they never say that organic is superior to conventional production, simply that organic uses practices that “foster cycling of resources, promote ecological balance, and conserve biodiversity”.  Though many of you may not believe it, conventional growing uses many of these practices too –  producers know that if they don’t pay at least some attention to sustainability then they will lose money over time.

So why am I talking about this today?  Well, I’ve had a few requests to discuss that new meta-study that came out a few weeks ago which showed that organic food has the same nutritional value as food produced conventionally.  Big deal.  Plenty of other meta studies have shown essentially the same thing –the quality of organic is LARGELY the same as conventional with a few nutrients (often vitamin C) a little higher in organic and a few (often protein levels) being higher in conventional.  Anyway, to make a long story short, I don’t know why this study got more press – maybe they have better PR people at Stanford where the study was put together.

Look, the reason that one food has more nutrients than another has much more to do with the food itself than whether the food was grown organically or conventionally.  No matter how you treat a McIntosh apple, it will never have as much vitamin C as a Granny Smith apple.  Period.  Folic acid will always be greater in bananas than grapes.  Period.  If you’re worried about getting enough of a particular nutrient then eat foods high in that nutrient.  If you’re worried about a lot of nutrients then eat a varied diet.

Of course the study also says that synthetic pesticides are more likely to be on conventionally produced foods than organically produced foods.  OK, I’ll buy that.  Makes perfect sense….but tell me, how much organic pesticide is on organically produced foods?  And how does it affect you?  If a farmer uses spinosad, an insecticide used by organic growers, it can be present at low levels in food, as can other organic pesticides such as pyrethrum.  But since residues of these organic pesticides are rarely tested you have no idea how much is in there.

Look, if you want to avoid pesticides on your fruits and veggies altogether and can’t grow a garden or go to a farmer’s market, then you should avoid foods where pesticides need to be used. These are the only foods where you can count on growers, organic or conventional, avoiding pesticides (No farmer WANTS to use pesticides – they’re expensive!).  To find foods where pesticides are less likely to be used just go to that crazy dirty dozen list which the Environmental Working Group puts out (which I think is a bit ridiculous – but I’ll leave that alone for now since this post is getting long) and select fruits and veggies from the clean 15.

In terms of organic production being better for the environment, as long as organic growers can use copper to control diseases, I’m concerned about how long term applications of this copper will affect
soils on land devoted to organic production over the long term.  I’m also concerned about fertilizer runoff and leaching in organic production – same as in conventional production.  Nitrogen and phosphorus from manure can and do run off just the same as nitrogen and phosphorus from synthetic fertilizer.

In both conventional and organic systems, the impact that production has on the environment comes down to the responsibility that a given producer takes for doing the right thing and protecting the environment.  To say otherwise is just silly.  There is so much leeway in the USDA organic system that there is plenty of opportunity for a USDA organic producer to do things that will make their operation significantly worse for the environment than a conventional producer of the same crops.

So…How Much Pesticide Is Actually In Our Fruits and Veggies?

We have discussed the dirty dozen here before – those foods which a group called The Environmental Working Group (wow—fancy name – everything they say must be true!) has established contain more residues of different pesticides than other foods.  I’ve already stated my concerns about selecting organic foods instead of conventionally grown ones because of a fear of pesticides so I won’t restate that here.  Instead what I want to call your attention to an article sent to me by our visiting professor, Charlie Rowher.  This article runs down the amounts of pesticides that are actually in the dirty dozen. And the thing is….there just isn’t much pesticide of any sort on most foods and there is no evidence at all that eating these levels of pesticides would be bad for us in any way – even if we ate them in copious amounts day after day.

To be honest I think the authors of this article go a little too far – I do think that there is some potential for damage even from the ultra-small pesticide doses that we find on our foods.  But their points are well taken – the amount of pesticides in food is miniscule and less likely to be damaging to us than a great host of other things.  I’m much more concerned about certain segments of our population suffering malnutrition from avoiding conventionally grown fruits and veggies than I am about the larger portion of our population getting cancer from eating them.


One of the best organic fertilizers out there – at least in terms of how plants respond to it —  is bat guano.  As most of you probably already know, bat guano is made of bat droppings.  What you probably don’t realize is that bat droppings need to be aged for a while in an arid environment before they become guano.  Caves provide the perfect environment for this to occur, and so that is where most bat guano comes from.

Because guano needs to be aged in special surroundings before it is used it is not a rapidly renewable resource.  Instead it’s kind of like peat in that it takes anywhere between decades and thousands of years for the raw material from which it is made to develop into the stuff that we use.  Furthermore, by harvesting bat guano we can actually damage the ecosystems present in the caves from which the bat guano is harvested.  Think about it – bats generally feed outside the cave, so when they defecate inside the cave they are actually bringing new nutrients into the cave – nutrients that other creatures can use.  Whole ecosystems are based on this poo!  So when we harvest bat guano from a cave what we are doing is disturbing a specialized ecosystem – a very unique system.

So am I encouraging you away from bat guano?  No more than I would encourage you to consider reducing your usage of peat – or of oil — or any other non-renewable resource.  I can’t deny that it’s a great fertilizer, but if you want to use an organic fertilizer why not at least consider one that is renewable instead of one that is from a limited resource and which may cause harm to a unique ecological system?