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How to Identify and Treat Herbicide Contamination of Commercial Soil, Compost and Manure

soil herbicide contamination danger sign

Over the last decade, there have been increasing reports from gardeners that their vegetables and flowers have been damaged or killed after adding manure or compost to their gardens, or when they’ve planted into new soil they had delivered. In fact, the problems of contaminated composts adversely affecting horticultural crops first surfaced in 1999.

The affected plants consistently show a consistent range symptoms, such as:

These symptoms are characteristic of herbicide damage, but it is important to keep in mind that they can be caused by various other factors, such as pests and diseases, and only specific plants are affected by these herbicides that contaminate commercial compost, manure and soil , so accurate diagnosis is important!

That said, herbicide damage of plants has a combination of symptoms that produces a characteristic look which horticulturists can usually identify quite readily.

The presence of herbicides can be verified by conducting a simple test at home to determine if soil, compost or manure is contaminated, which is detailed later in this article, along with a list of plants which are affected by these herbicides.

Deformed leaves due to herbicide damage (source: Oregon State University Extension, modified by Deep Green Permaculture)

Which Herbicides Are Implicated in Manure, Compost and Soil Contamination?

The herbicides (weedkillers) involved in nearly every case of herbicide contamination of commercial manure, compost and soil, as well as the contamination of grass clippings and hay on farms, are aminocyclopyrachlor, aminopyralid, clopyralid, picloram, fluroxypyr and triclopyr, which belong to a class of herbicides known as synthetic auxin herbicides, as they mimic the natural plant hormone auxin and disrupt plant growth of sensitive broadleaf plants – they don’t affect all broadleaf plants and do not affect most grasses.

Synthetic auxin herbicides have been used for many decades, and even the older generations of these herbicides which are less potent and persistent have been problematic and implicated in compost, manure and soil contamination, and still are to this day (the most recent case in Melbourne, Australia was in Feb 2021, at the time this article was written).

The newer generations of these herbicides are much more toxic and persist much longer, thereby increasing the risk and extent of compost, manure and soil contamination risk by orders of magnitude. We can see from the table below that these newer synthetic auxin herbicides typically belong to the pyridine‐carboxylate, pyridyloxy‐carboxylate and pyrimidine‐carboxylate chemical sub-classes.

Subclasses of synthetic auxin herbicides and their year of introduction








These herbicides are used on pastures and forage crops where animals are grazed, grain crops, certain fruits and vegetables, and non-crop areas such as commercial turf, wildlife and habitat management areas, forestry, industrial sites, and rights-of-way. Some are also used on seasonally dry wetlands, including ditch banks, dry ditches, and dry canals, and are applied up to the edges of aquatic areas to control weeds along creeks, streams and around stock ponds.

Based on toxicity and environmental fate data submitted by the manufacturers of these herbicides to USDA-EPA, the European Union agency and the Australian APVMA to support the registrations their products, government regulators have approved the use of these chemicals on grazing land, and have decided that livestock, including animals raised for meat or other products destined for human consumption, can safely consume hay and/or graze in treated pastures, as they have rated these herbicides very low in mammalian toxicity.

Now, this is where the problem starts…

How Synthetic Auxin Herbicides Contaminate Compost, Manure and Soil

These synthetic auxin herbicides bind to the lignin in pasture grasses. Lignins are a class of polymer compounds that most plants use in their cell walls and other tissues for structural support. When animals graze they ingest the herbicides, which passes straight through their digestive tract without breaking down, and are excreted out in urine and manure. These herbicides remain bound to the large amounts of undigested grass residues which are present in the manure, and are released into the environment as the plant matter decays.

Having a high soil mobility, these herbicides leach into the soil with rainfall, irrigation, and dew. They can be carried by water, and wash downhill to offsite locations to affect non-target plants. They have the potential to move towards groundwater and contaminate surface water.

As with many other highly-persistent herbicides, they can remain active in contaminated soil, manure, compost, hay, straw, and grass clippings for very long periods of time.

These herbicides are eventually broken down by soil microbes, heat, moisture, and exposure to sunlight, and their breakdown can take from one month to several years, depending on environmental conditions. Typically, they don’t break down very easily though. They can stay active in manure even after it has been composted, and persist after contaminated green waste has been processed through a commercial composting facility! Also, microbial activity decreases with soil depth, so these herbicides have the potential to persist longer at deeper soil levels.

Some field reports have indicated that complete deactivation can take several years, and hay has been reported to have residual herbicide activity after three years when stored in dry, dark barns. Breakdown of these herbicides is particularly slow in piles of manure and compost, , due to lack of oxygen.

Both fluroxypyr and triclopyr are much less persistent than aminocyclopyrachlor, aminopyralid, clopyralid, and picloram, but they are still rated as highly persistent herbicides and can damage non-target plants in the same way.

Just to make matters worse, the older synthetic auxin herbicide dicamba has a high vapour pressure, making it one of the most volatile herbicides, that is prone to vaporizing, or volatizing, and drifting through the air, affecting crops miles away from its site of application. The potential for dicamba vapour drift is greatest under hot and dry conditions during and for 2-3 days after application. As a historical note of interest, in the US in 2017, an estimated 3.6 million acres of farmland were damaged by dicamba, a lawsuit followed and the manufacturers of the product reached a $400 million settlement with farmers.

Which Plants Are Sensitive to Synthetic Auxin Herbicides?

Synthetic auxin herbicides do not affect all plants, only certain plants are susceptible, but those affected include a wide variety of edible and ornamental plants.

Crops known to be sensitive to picloram, clopyralid or aminopyralid include:

* affected by aminopyralid and picloram only.

Broad beans affected by clopyralid herbicide contamination (source: Corteva Agriscience)
Tomato affected by aminopyralid herbicide contamination (source: Corteva Agriscience)
Potato affected by aminopyralid herbicide contamination (source: Corteva Agriscience)
Dahlia affected by clopyralid herbicide contamination (source: Corteva Agriscience)

Why Doesn’t Commercial Hot Composting Break Down Synthetic Auxin Herbicides?

If synthetic auxin herbicides are broken down by soil microbes, heat, moisture and exposure to air, shouldn’t they degrade quickly in commercial composting facilities which use hot composting systems which have all of these factors in abundance and are able to degrade many synthetic organic chemical contaminants?

Commercial composting facilities create conditions where the temperature stays in the range of 49-77 °C (120-170 °F), and moisture levels are kept between 40-60% during the active composting period to support the micro-organisms which break down the waste.

If we look at the melting points (MP) and boiling points (BP) of the range of synthetic auxin herbicides listed below, we see that none will not melt nor boil at commercial composting temperatures, let alone degrade. Only 2,4-D decomposes at its boiling point which is a very high 160 °C, which is more than twice the composting temperature.

The temperatures of commercial hot composting systems simply are nowhere near hot enough to degrade these herbicides.

Subclasses of synthetic auxin herbicides, their chemical names and respective melting points (MP) and boiling points (BP)








Why Trace Amounts of Synthetic Auxin Herbicides Cause So Much Damage to Plants

The reason the synthetic auxin herbicides are names as such, and are so potent in minute quantities, is because at low concentrations they mimic several of the physiological and biochemical effects of the natural plant hormone indole-3-acetic acid, which is usually referred to as auxin or IAA.

The auxins are a class of plant hormones found in all plants, and are responsible for regulating the amount, type and direction of plant growth. These natural plant hormones are mostly found at the tips of plant shoots and roots, where the most active growth occurs.

These plant growth regulator (PGR) herbicides act as auxin-mimics, they enter plants through their leaves and roots, where they are absorbed by plant tissues and are translocated to the meristematic (high-growth-rate areas of the plant such as shoots and roots tips) where they accumulate, replacing the natural auxins at binding sites where they act, causing abnormal growth and disrupting the growth processes of the plant. This leads to rapid, uncontrollable growth which results in vascular tissue destruction, until the plant literally “grows itself to death”, which usually occurs within a few days or weeks.

These herbicide are usually sprayed on grasses to control broadleaf plants growing amongst them. Grasses are generally not affected because they are highly tolerant to this class of herbicide, as they can rapidly metabolize them and sequester (bind) them in special parts of the cell so they cannot exert their herbicide action. Many broadleaf plants are unable to metabolise and sequester the herbicide and therefore succumb to the effects of the herbicide.

A very miniscule residue of these persistent pyridine carboxylic acid herbicides, as little as 1 part per billion (ppb) in soils and growing media, can cause significant damage to plants. This concentration corresponds roughly to around half a teaspoon (2.5ml) of herbicide into an Olympic-sized swimming pool (2,500,000 litres).

Since this group of herbicides can produce toxic effects in plants at concentrations as low as 1 to 10 parts per billion, they are difficult to detect because, at the present date, no commercial testing laboratories can reliably detect or measure these compounds at such low low levels. The problem of measurement is compounded by the fact that these herbicides binds to plant lignin, and that the complex nature of composts and plant materials makes the recovery and analysis of herbicide residues difficult. Seed germination tests using sensitive plants can be used to detect such low levels of these herbicides, and the process is described later in this article.

For those interested in the chemistry, these auxinic herbicides have a chemical structure similar to the natural plant hormone IAA, as shown in the diagram below. These herbicides were classified into three different classes based on the position of the carboxylic acid moiety and the type of aromatic group they possess, (1) phenoxyalkanoic acids (e.g., 2,4-D, MCPA); (2) benzoic acids (e.g., dicamba, cloramben); and (3) pyridine carboxylic acids (e.g., picloram, clopyralid, triclopyr and fluroxypyr). More recently, the classes have been revised and expanded, so that triclopyr and fluroxypyr are now classed as pyridyloxy-carboxylates, aminocyclopyrachlor as a pyrimidine-carboxylate, chlorfenac and chlorfenprop as phenyl carboxylates, just to mention a few of the changes.

Auxinic herbicides have a chemical structure similar to the natural plant hormone IAA

How Long Do Synthetic Auxin Herbicides Really Last in the Soil?

To clear up any misconceptions about the potency of these herbicides, and any marketing misinformation downplaying their persistence, I randomly selected one of the agricultural formulations, and examined the directions on the label, which are very extensive as the manufacturers spell out the facts very clearly to avoid legal liability.

Hotshot Herbicide ACTIVE CONSTITUENTS: 10 g/L AMINOPYRALID present as triisopropanolamine salt SOLVENT: 140 g/L FLUROXYPYR present as methylheptyl ester 418 g/L LIQUID HYDROCARBON

Northern New South Wales & Queensland

Plant-back periods for rotational crops following application of Hotshot for rates up to 750 mL/ha on black cracking clay soils. These plant-back periods are based on normal rainfall pattern. During drought conditions (or when rainfall is less than 100 mm for a period of 4 months or greater) the plant-back period may be significantly longer.

Winter Crop Plant-back Period

Summer Crop Plant-back Period

NOTE: What this is saying is that when this herbicide is applied at a rate of 750 mL/ha, that’s a mere 3/4 of a litre over 1 ha = 10,000 m² in tropical climates with high rainfall, the soil is not safe to plant into for 4-9 months, depending on the crop, with a 6-9 month plant back period for plants classed as sensitive to this herbicide.

Southern New South Wales, Victoria, South Australia & Western Australia

Plant-back periods for rotational crops following application of Hotshot for rates up to 500 mL/ha.

Crops Plant-back Period

NOTE: When we look at temperate climates with lower rainfall, even less of this herbicide, applied at a rate of 500 mL/ha, that’s a only 1/2 litre over 1 ha = 10,000 m², the soil is not safe to plant into for 9 months with non herbicide sensitive plants, and plant back period for plants classed as sensitive to this herbicide is 20 months, which is one and three quarter years!

How to Test for the Presence of Synthetic Auxin Herbicides in Soil, Compost and Manure

Laboratory tests for the presence of these herbicides are generally expensive and usually cannot detect the trace amounts of synthetic auxin herbicides that can adversely affect plants.

A more sensitive test is a plant bioassay that can be performed at home. This simple pot bioassay involves growing peas, beans, or tomatoes, all of which are very sensitive to the presence of these herbicides, in the the commercial soil, compost or manure that is suspected to be contaminated, alongside appropriate controls.

Simple Pot Bioassay for Detecting Herbicide Contamination

Step 1 – Take a number of random samples from throughout the pile of commercial soil, compost or manure that is being tested using a hand trowel, being sure to get deep inside the pile. The more samples that are taken, the better, take at least 20 samples per pile, as they will be more representative of the whole pile of materials being tested.

Step 2 – Mix the samples together for the pile being tested, making sure to mix thoroughly. Note: If there are separate sources of soil, being tested, don’t mix them, perform this test separately for each, labelling each test to identify the source or locations of materials being tested.

Step 3 – Fill several 10cm (4”) pots with only the commercial potting mix containing fertilizer, these will be the control pots. Label them as ‘control’.

Step 4 – Fill three to six 10cm (4”) pots with a 1:1 mixture of the soil, compost or manure with a commercial potting mix containing fertilize, these will be the test pots. To do this, first make a mixture of 50% commercial potting mix and 50% of the soil, compost or manure being tested, mix it together thoroughly, and fill the test pots with it.

Step 5 – Place saucers underneath each pot, or position the pots far enough apart so that water running out of the bottom will not reach another pot, as these herbicides are very water soluble and will be carried in any runoff from the pots and be absorbed by any pot sitting in that water..

Step 6 – Using either bean, pea, or tomato seeds for every pot in this test, plant three seeds in each pot evenly spaced apart, at a depth twice the height of the seed, water, and let them grow for two to three weeks. There should be at least three sets of true leaves after the first pair of dicot leaves on the seedlings when they are ready to assess.

Step 7 – Interpret the test results:

Pea plants herbicide damage, with leaf curling indicative of slight herbicide damage (source: Washington State University, 2011)
Pea plants showing herbicide damage, with leaf curling and stunted plants indicative of severe herbicide damage (source: Washington State University, 2011)

Simple Field Bioassay for Detecting Herbicide Contamination

A simple bioassay can be performed onsite in a field or garden site to determine if there is herbicide present due to the application of contaminated soil, compost, manure, hay, or grass clippings.

To conduct a field bioassay, plant peas or beans in short rows, scattered throughout the affected area to be tested.

If herbicidal symptoms appear, such as leaf cupping, distorted new growth and twisted stems, then that is indicative that synthetic auxin herbicide contamination has occurred. Do not plant sensitive plants, plant grasses instead, then test again the following year to determine if the herbicide is still present in the soil.

On the other hand, if the test plants grow normally, it should be safe to grow any broadleaf crops.

Seed Germination Field Soil Bioassay for Detecting Herbicide Contamination

The following bioassay is from the directions for the Dow AgroSciences Hotshot herbicide, a mixture of the synthetic auxin herbicides aminopyralid and fluroxypyr.

  1. A simple bioassay can be conducted by collecting at least 10 spade spits of soil to a depth of 200 mm from around the paddock and thoroughly mixing the soil together.
  2. Place some of this soil in a shallow container to a depth of 3-5 cm and sow 100 seeds of the susceptible plant to be grown (subterranean or white clover is a good indicator plant where it is not practical to use the susceptible plant) into the soil.
  3. Keep in a warm and well lit location and ensure the soil does not dry out.
  4. After crop emergence, check the number of plants that have germinated and seedling vigour.

Symptoms of Hotshot residues include non-germination or low plant emergence, leaf cupping, leaf whitening, stem elongation and twisting. If these symptoms occur-do not grow the susceptible plant. Repeat the bioassay again after a further time interval.

How to Treat Soil Contaminated with Herbicides from Commercial Soil, Compost or Manure

What can you do if you test for herbicide contamination and find that synthetic auxin herbicides are present in the soil?

1. Plant a grass crop to absorb the herbicide from the soil. Grasses are generally not sensitive to synthetic auxin herbicides and will bind them, which is the cause of the problem in the first place, but also a solution for bioremediation. Use grasses that are commonly used as green manures, as they’re easy to source, such as warm season green manure grasses – Buckwheat (Fagopyrum esculentum), Japanese Millet (Echinochloa esculenta), Millet ‘French White’ (Panicum miliaceum) and cool season green manure grasses such as Oats (Avena sativa). The grass can be clipped and discarded into the landfill waste bin, don’t put them into the green waste recycle bin or dig them into the ground as this will re-release the herbicide!

2. Add activated charcoal and Zeolite to contaminated soil to absorb herbicides. This is not the most cost-effective option but it will bind up the herbicide so it will unavailable to plants and in its bound state can be gradually broken down by soil microorganisms.

3. Make biochar and incorporate it into the soil to absorb and bind herbicide contamination. Biochar is form of activated charcoal which provides many additional benefits and can significantly improve soil health and productivity. It can be produced onsite in very large quantities using a home-made biochar kiln, an ideal solution for larger properties and farms with plenty of timber lying around.

4. Incorporate manure evenly into the soil surface to encourage soil microbial activity and promote herbicide decomposition.

5. Add worm casting liquid to the soil, also known as ‘worm wee’, it’s the dark liquid leachate that is produced by worm farms, and it’s full of beneficial microbes that are involved in the breakdown of organic matter. Dilute it 10:1 or more with water so it’s the colour of weak tea, and preferably use rainwater as it doesn’t contain chlorine or chloramine which can kill bacteria.

6. Use supplemental irrigation, basically increase watering, as the breakdown of synthetic auxin herbicides in plant residues or manure is more rapid under warm, moist soil conditions.

7. Remove contaminated material when contaminated manure or mulch has been applied, as the material will keep releasing herbicide residue as it breaks down. Scrape off any loose manure or compost and put it into the landfill waste bin (not the green waste recycle bin!) or spread it on grassland.

8. Soil removal is an option for very small areas as it’s a very laborious process. The herbicide contaminated soil can be removed and spread on grass or pasture areas that will not be harvested as animal feed, or along fencerows and other sites where the herbicide can legally be applied. (Note – this doesn’t sound like the most environmentally sound option!)

9. Soil addition can be used for larger areas or large quantities of soil. By adding more soil, the ratio of contaminated compost/manure to soil is reduced, reducing the herbicide exposure and concentration in the area. (Note – I think this strategy is not viable as it is very costly and the synthetic auxin herbicides will not be diluted out enough considering the extremely low concentrations that are phyotoxic!)

10. Tilling the soil to speed up the rate of breakdown. Dig through or rotovate the herbicide-contaminated soil several times, preferably between summer and autumn when the soil is at its warmest to fully incorporate contaminated compost or manure into the soil and increases microbial activity which breaks it down. The herbicide residue levels in the soil will peak at three weeks after digging due to release from contaminated plant matter as it breaks down. This is a recommendation from the RHS.

After using any of these methods to reduce the herbicide contamination of the soil, always retest the soil, conduct the bioassay tests described above, to determine whether the herbicide is still present or not before any replanting decisions are made.

For more information on herbicides and alternatives, see these related articles:


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