Use of Disinfestants to Control Plant Pathogens

*USDA ARS Thad Cochran Southern Horticultural Laboratory, Poplarville, MS,

Mention of trade names or commercial products here is solely for the purpose of providing scientific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.

What you cannot see, sometimes can hurt you, and plant pathogens are one of those threats that are too small to see. You have multiple tools available to help prevent or manage disease and minimize plant losses. One of those tools is sanitation, and one group of products commonly used for sanitation are disinfestants (Copes 2018). Disinfestants are biocides that kill oxysporum micro
organisms on the surface of inert materials, such as wood benches, galvanized metal benches, and plastic containers, as well as on plant tissues. In both general and scientific literature, the terms ‘disinfectant’ and ‘disinfestant’ will be found referencing the same products and the same chemical activities. The term ‘disinfestant’ more accurately reflects how these products work and will be used exclusively in this article. This article will cover disinfestant usage in ornamental plant nurseries and greenhouse plant production and may be useful for other situations.

This article will focus on factors affecting the efficacy of disinfestants. The disinfestants commonly used in plant production are listed in Table 1. Safety and environmental regulations pertain to these products just as to other pesticides. Recommendations listed on disinfestant labels should be followed. Each product has advantages and disadvantages that effect their suitability for particular microorganisms, uses, and environmental conditions. Relevant usage and efficacy information is given in Table 1 based on available data. See Copes (2018) for a more comprehensive list of literature cited.

In this article, disinfestants will be referred to by the common chemical name when referring to them collectively or generally and by trade names when referring to a specific product. Chemical nomenclature will not be used in this article. However, rates of bleach will be referred to as a percent of the active ingredient (a.i.) of sodium hypochlorite (NaOCl). This is used to avoid confusion caused by using percent bleach, since bleach products contain different percent’s of NaOCl.

General steps to treating production surfaces and tools with disinfestants.

There are up to 5 steps to successfully treat production surfaces and equipment: remove all organic and inorganic matter and debris, clean surfaces, leave production areas fallow or empty for a time, select an appropriate disinfestant, and expose the pathogen to the disinfestant for the needed contact time.

  1. Remove debris, such as leaves, organic media, and soil from tool surfaces and production areas using a brush, broom, air blower, or moderate pressure water hose.

    The reason why. Disinfestants are highly reactive chemicals that can react with inorganic and organic matter. A disinfestant solution contains only a fixed amount of the active ingredient (a.i.). Some proportion of the a.i. is consumed when it reacts with inorganic or organic matter and surfaces, eventually causing a drop in a.i. below a lethal dose. Soil and organic matter also can physically shield microorganisms from coming in contact with the disinfestant.

    Precaution. If pathogen propagules are present in debris, then the debris itself needs to be collected and discarded to a refuge pile that is downwind, downhill and a sufficient distance from plant production areas, so the pathogen is not introduced back into the production system.

  2. Clean surfaces with a detergent. Rinse thoroughly with clean water.

    The reason why. This removes organic films and gummy substances that hold pathogens and removes part of the pathogen inoculum on bare surfaces. In the case of less threatening disease problems, cleaning may be sufficient to achieve adequate sanitation.

  3. Leave production areas empty for 4 or more weeks.

    The reason why. The UV radiation from sunlight and/or high temperatures can kill many pathogen’s propagules on production surfaces. This step can be useful but is not necessary, so usage should depend on your production schedule, facilitates, environment, and the pathogen involved. When outside temperatures are high enough, closing doors and openings will trap sunlight and increase greenhouse or hoop house temperatures, such as during the summer in the PNW.

    Precaution. Some pathogen propagules are likely to survive in hidden areas, such as under surfaces and in crevices, thus require use of disinfestants.

  4. Select a disinfectant that has been shown to work against the pathogen(s) of concern with your crop(s) and on the surface being treated. If such information is not available, select one with broad activity. The most common products used to disinfest surfaces in agricultural production contain the following active ingredients: chlorite (potassium or sodium), hypochlorite (sodium or calcium), hydrogen peroxide (= hydrogen dioxide) plus peroxyacetic acid, and quaternary ammoniums (Table 1). A few additional products are listed that are used for specific applications.

    The reason why. Not every microorganism is equally sensitive to a disinfectant.

  5. Apply disinfectant correctly, using information on product labels, in this article, and other educational extension articles.

The reason why. The concentration of a disinfectant and the length of time the pathogen is exposed to it are requirements for killing pathogen populations. Generally, the recommended rates will be effective against many pathogens.

Precaution for treating production and tool surfaces.
Most products specify a contact duration on the product label (summarized in Table 1). Contact time is easily followed with submergence tanks, but difficult to achieve when treating surfaces. Maintaining a contact time on rapidly drying surfaces requires reapplication of multiple light applications to maintain “shiny” wet surfaces for the specified time, such as 10 min. One suggestion is to spray disinfectant on a section of a production surface, then move back to the starting point before it starts to dry and repeat the process several times to maintain the proper contact time. Repeat that application process on other sections, until the larger area is treated. Larger areas can be treated more quickly under cloudy, cooler conditions, because surfaces dry more slowly. Be mindful of toxicity from elevated vapor concentrations in closed greenhouse spaces because human, plant, and equipment safety can be at risk with upper label rates or extended application periods.

Factors affecting efficacy of disinfestants.

A common misconception is that disinfectants are broad spectrum sterilants that kill all microorganisms present. Microorganisms vary in sensitivity to any given chemical, and as a result different disinfectants and/or rates may be needed to properly inactivate or kill propagules of a specific pathogen genus or species. This information is not broadly documented, but has been clearly demonstrated (Koponen et al. 1992, Mebalds et al. 1997). Mebalds et al. (1997) reported that the lethal activity of bleach varied from 0.2% to 5.25% for viruses, 1% to 10% for fungi, and from 10% to 12.5% for bacteria. Microorganisms also can vary in their sensitivity to disinfectants due to environmental conditions (such as temperature, pH, and dissolved oxygen). Microorganisms generally absorb disinfectants rapidly between 68°F and 86°F. Use disinfectant recommendations developed for specific microorganisms, when available. The term ‘inactivate’ is commonly used in scientific literature because the term addresses uncertainties in measuring recovery and viability of different microorganisms that are found in different habits, such as viruses in cell sap on a surface versus in living host cells. The general term ‘kill’ will be used in place of ‘inactivate’ in this article.

A number of problems can influence disinfestant activity (Table 1). Chemical decomposition of a.i. can occur in seconds to minutes in response to water characteristics (such as pH, concentrations of mineral and organic compounds, water hardness, and temperature); and due to reactivity to production surfaces (metal, plastic, and wood). These same factors reduce longevity of the a.i. when mixing disinfestant solutions in spray tanks, treating irrigation water, and soaking materials (such as containers and produce) in dump tanks. In dump tanks, additional loss of a.i. can occur over a period of hours due to increased evaporative loss from wind and chemical degradation from sunlight. Disinfestant solutions in dump tanks need to be changed or recharged periodically because of these reasons, for example bleach solutions need to be changed every hour.

When submerging products, such as containers, in a disinfestant solution, it is critical to dislodge all air bubbles or air pockets by shaking and tilting the containers allowing air bubbles to escape. Air pockets prevent the disinfestant solution from contacting that part of the container, as a result the containers are not being uniformly treated. One approach is to orientate stacked containers with the large opening up, swirl the stacks inclining them in various angles to dislodge air bubbles, and place a heavy screen on top to keep containers submerged.

Howard et al. (2007) reported several considerations when selecting a disinfestant due to differences in pathogen sensitivity, plant toxicity, reactivity to material surfaces, and corrosiveness. Differences in disinfestant efficacy due to the material surface being treated has been documented previously (Copes 2004, Koponen et al. 1992). For example, the percent Botrytis conidia killed was nearly equal when spraying bleach on plastic, metal, and pressure-treated wood surfaces, but less effective on untreated wood. The quaternary ammonium compound (QAC) had the highest activity on metals, slightly less on plastics, and was ineffective on untreated wood. Hydrogen dioxide was ineffective at the preventative rate, but uniformly effective on plastics, metals, and pressure-treated wood at the curative. However, a total kill of Botrytis conidia on production surfaces required higher than label rates for the QAC and hydrogen dioxide, especially on untreated wood. Results vary between studies and between organisms. In contrast to the previous statements, Fusarium spp. inoculum has been eliminated from wooden stakes with high pressure washing and several sanitizing agents, including bleach products.

While most of this information focuses on loss of disinfestant activity, pathogens can also develop resistance to these chemistries. Resistance to many classes of disinfestants has been well documented in bacteria, fungi and viruses with human pathogens, food contaminants, food yeasts, industrial fouling, and water-line biofilms, but to the authors knowledge has not been documented with plant pathogens. If chemical effectiveness is a problem, switch to a disinfestant from a different chemical class and consult a plant pathologist or crop advisor.

Treating surfaces of tools, equipment and structures

Washing and applying disinfestants are the main tools used to disinfest hard surfaces.


Tools become contaminated by contact with infested rooting media, soil, or plant material. Any tool (mechanical pruners, trowels, shovels, fertilizer dispersers, motorized shears, tagging machines, etc.) that may have been exposed to pathogens should be cleaned and disinfested prior to moving to another site or block of plants. Contamination of cutting tools should be a constant concern, since they easily acquire and carry pathogen propagules from infested or diseased plants to healthy plants. Shovels and trowels should be disinfested to prevent carrying pathogens into a non-contaminated area. It is commonly recommended that tools be soaked for 2 min, although product labels should be checked.

Bleach, QACs, peroxygen compounds, and alcohols are common disinfestants used for treating tools (Celar et al. 2007, Olivier et al. 2015), and some examples follow. It is important to realize some pathogens are easier and some harder to eliminate from tools. Contaminated pruners soaked in a 0.525% NaOCl for 2 sec killed Erwinia amylovora spread from infected apple stems, and for 1 min killed tobacco mosaic virus (TMV) spread from infected petunia. Immersing metal tools for 15 min in 0.525 % a.i. NaOCl was consistently more effective than five other disinfestants at killing potato spindle tuber viroid; however, none of the treatments eliminated the viroid. Soaking pruners in 20% wt/vol of nonfat dry milk plus 1% Tween 20 was as effective as 0.525% a.i. NaOCl in killing TMV obtained from petunia, but again, neither treatment totally prevented virus transmission to petunia from contaminated tools. Potato virus Y (PVY) particles were more consistently eliminated from pruner blades with a 2 sec immersion in 0.525% NaOCl than a 15 sec immersion in 1% QAC. To minimize corrosiveness caused by bleach, all metal parts of the pruners need to be washed and coated with oil following bleach treatment. Alternative, less corrosive choices, include alcohol (isopropyl or ethanol) and QACs.

Plant Containers

Reuse of plant containers is risky, because pathogens could have produced aggregates of propagules, including difficult to kill survival structures that could tightly adhere to the container. Pieces of potting mix or plant debris attached to the container can further protect pathogens from chemical disinfestants. Using new containers provides the surest way to avoid this type of contamination. Placing disposable plastic inserts into reused Styrofoam transplant trays has been shown to prevent pathogen transmission.

If containers are to be reused, they should be thoroughly washed to remove all soil, organic media, and plant tissue. Cleaned containers should be submerged in disinfestant for 10 to 30 min or treated with steam 150°F to 160°F for 45 to 60 min. Removing debris by washing followed by soaking in a disinfestant was done in all of the following studies. QAC (KleenGrow) was more effective at killing Thielaviopsis basicola spores than bleach, another QAC (GreenShield) or hydrogen peroxide (ZeroTol). Thielaviopsis basicola was killed on plug trays either by spraying trays with a 1 to 50 ratio of ZeroTol to water solution, or submerging plug trays in 0.525% NaOCl for 10 min. Flats used for growing tobacco seedlings infected with T. basicola were killed with steam. Spray application of 0.525% NaOCl consistently reduced microconidial densities of F. oxysporum f. sp. callistephi on styrofoam to an undetectable level. Soaking plastic irrigation stakes in bleach or a QAC reduced populations of F. oxysporum f. sp. radicis-lycopersici to an undetectable level. Fusarium oxysporum f.sp. radicis-lycopersici was reduced to an undetectable level from styrofoam trays with steam treatment (160°F for 45 min) but not with bleach or QAC.

Equipment (conveyers, trailers, transplanters, etc.)

Preventing spread of pathogen propagules on large equipment to a new area where a susceptible crop is being grown can be a highly effective prevention technique. This applies to diverse pieces of equipment, such as automated seeding machines, conveyers, irrigation pipes, sprayers, tractors, trailers, and transplanters. Factors to consider include the likelihood that equipment is contaminated with a pathogen, the potential for crop loss, the potential rate of spread from the contaminated area, and the difficulty of eradicating the introduced pathogen. With seeders and transplanters, cleaning may be needed when plant types are changed. With conveyors, trailers, carts, and racks, cleaning and disinfesting equipment should be planned as part of the plant-
transfer activity after handling plants that have a history of disease and prior to handling plants prone to the same disease.

With large equipment, cleaning and sanitizing may be divided into six steps: (1) dry removal of gross contamination and solids, (2) wet washing and solvent washing, (3) rinsing, (4) drying, (5) disinfesting, and (6) machine maintenance. More specific efforts may be required with certain pathogens including quarantine status pathogens. Decontamination of important pathogens should only be done on the site where the contamination occurred to reduce the possibility of unintentionally spreading disease to off-site locations. A sanitizing station can be used to contain an area for cleaning.

A sanitizing station is a containment area. A sanitizing station inside a facility should be set up on an impermeable floor. If the sanitizing operation is adjacent to plant production areas, a wall of plastic sheeting should be hung either from a temporary wall frame of wood or metal tubing or from overhead structures. Depending on the pathogen, water should be directed to flow into a drainage system or sump well for later treatment and removal if needed, or contained in a barrier and mopped into containers for later treatment and removal. Drums or plastic containers can be used to contain spent cleaning and disinfestant fluids. The area needs to be cleaned and disinfested after equipment treatment has been completed.

An outside sanitizing station should be separated from normal vehicle traffic flow and plant production areas. The cleaning and disinfesting procedures should be done at the site where contamination of diseased crops occurred. Sanitizing stations should consist of an impermeable layer, such as a layer of plywood covered with thicker than 2-mil plastic sheet; a berm [such as 4 x 4-inch wood, sand tubes, sand bags, etc.]; framing materials to build the containment structure; a sump pump and power supply; and drums or plastic totes to contain spent cleaning and disinfesting fluids.

Production and greenhouse structures.

Sanitation begins outside the greenhouse. All weeds around production areas should be removed to prevent refuges for pathogens and insects that can transmit them. Areas of grass can be planted for a 10-ft distance around a greenhouse. Insect screening should be used to cover vent and fan openings to exclude insect vectors. Screen mesh sizes should be selected to optimize insect exclusion while allowing adequate airflow. Additionally, plastic sheets and screening are available that maintain high transmission of visible light while blocking portions of the ultraviolet spectrum, which interferes with the ability of insects to orient and find plant hosts. Insects can easily enter through the opening of hinged doors. A simple double-door entrance with a small entryway can be used; additionally this double door provides a positive pressure balance between outside doors and the greenhouse facility.

Foot baths should be located at access doors and used to prevent potential pathogen-infested soil and debris from being carried inside (Gullino et al. 2015). Foot baths vary from depressions in walkways to tubs. Prior to using a foot bath, rinse and wipe debris from shoes or use shoe covers that can be immersed in the solution for 30 sec to 3 min depending on the disinfestant label. Disinfestant solutions in foot baths should be changed daily, since many products, such as QACs and peroxy compounds, are less effective when plant matter or soil is present. Phenols react less with organic matter.

Greenhouse interiors should be routinely sanitized, since some pathogens can survive for years in soil and over a month on metal, rubber, and wood surfaces. At least annually, wash upper greenhouse structures, walls, benches, and floors, and treat with a disinfestant. For algal problems select disinfestants such as peroxy compounds, QACs, and bleach. QACs were very effective against fungal pathogens on most greenhouse surfaces, other than some synthetic materials, like polyethylene (Mebalds et al. 1997). To sanitize greenhouse sections, remove all plants and organic and inorganic debris from benches and floors.

Disinfestant activity is more reliable on nonporous surfaces, such as metal and plastic materials. Benches made with pressure-treated wood structure may be more difficult to disinfest. For example, a 10% bleach solution was effective against many pathogens present on metal and plastic surfaces, while a 20% bleach solution was needed to inactivate Thielaviopsis basicola and Botrytis cinerea on pressure-treated wood.

If soil floors exist under greenhouse benches, cover soil with gravel so no soil is exposed, because soil can harbor pathogens, shore flies, and fungus gnats. Areas with gravel can be first covered with ground fabric. Drips from condensation on the roof, from leaks in the roof, and from water lines can generate enough splash force to collect and carry pathogen propagules from the soil onto crops on benches or from container-to-container; therefore, the occurrence of drips should be minimized. Hose nozzles and watering wands should never come in contact with the floor and should be cleaned and allowed to air dry periodically. Install enough hose-end holders so hose nozzles can be conveniently kept off the ground and uncontaminated.

Sanitation practices are easier to implement if pots and trays are set on top of benches. Due to the cost of benches, some businesses set pots and propagation trays directly on polyethylene or gravel floors. In such cases, sanitation is more difficult, but still can be done. Organic matter should be removed because it can serve as a habitat and food source for pathogens. The bulk of organic matter can be removed with a broom or blower. Brooms should be sanitized afterwards to prevent pathogen spread to other areas of the operation. Blower direction needs to be considered so pathogens are not blown out of the house into surrounding areas of the operation. Cleaning the floor and lower walls with soap and/or water further removes small particles of organic matter. Spraying a disinfestant on the floor and walls further reduces persistence of pathogen populations on those surfaces.

In the case of high-tunnel greenhouses and some shade houses, plants are grown directly in soil. A number of plant pathogens naturally survive in the soil environment. Populations of soilborne plant pathogens can be controlled between crops using heat, fungicides, and/or fumigants. Consult other sources for further information.


Celar F., Valic N., Kosmelj K., Gril T. 2007. Evaluating the efficacy, corrosivity and phytotoxicity of some disinfectants against Erwinia amylovora (Burrill) Winslow et al. using a new statistical measure. J. Plant Dis. Protect. 114:49-53.

Copes W.E. 2004. Dose curves of disinfestants applied to plant production surfaces to control Botyrtis cinerea. Plant Dis. 88:509–515.

Copes W.E. 2015. Spread potential of binucleate Rhizoctonia from nursery propagation floors to trays containing azalea stem cuttings and sanitary control options. Plant Dis. 99: 842–847.

Copes, W.E. 2018. Sanitation for Management of Florists’ Crops Diseases. Pages 1-37 in: Handbook of Florists’ Crops Diseases. R. J. McGovern and W. H. Elmer (eds.) Springer, Berlin Heidelberg, Germany. DOI: 10.1007/978-3-319-32374-9_9-1. 20.

Hochmuth R.C., Sprenkel R.K. 2015. Exclusion methods for managing greenhouse vegetable pests. Entomology and Nematology Department, UF/IFAS Extension Bulletin ENY-846.

Gullino M.L., Daughtrey M.L., Garibaldi A., Elmer W.H. 2015. Fusarium wilts of ornamental crops and their management. Crop Protect. 73:50–59.

Howard R., Harding M., Savidov N., Lisowski S., Burke D., Pugh S. 2007. Identifying Effective Chemical Disinfectants for Use in Sanitizing Greenhouses. Interim Progress Report III. Alberta Professional Horticultural Growers Congress and Foundation Society. (accessed Nov 2, 2015).

Koponen H., Avikainen H., Tahvonen R. 1992. The effect of disinfectants on fungi in pure culture and surface materials. Agric. Sci. Finland 1:587–596.

Olivier T., Sveikauskas V., Grausgruber-Gröger S., Virscek Marn M., Faggioli F., Luigi M., Pitchugina E., Planchon V. 2015. Efficacy of five disinfectants against Potato spindle tuber viroid. Crop Protect. 67:257–260.

Mebalds M., Tragea W., van der Linden A. 1997. Disinfestation protocols for equipment used in the nursery industry. Horticultural Research & Development Corporation, Gordon, NSW, Australia. Publication No. NY61.

Table 1. Partial summary of some pertinent information about disinfestants, which is not a substitution for reading the label.









Trade names of
products commonly
used in ornamental
plant production

Clorox, bleach,
chlorine gas




Green Shield

many others

Numerous products so none named



Glutex GS1


Organism activity a

F, Bvs, Ven, A

F, Bvs, Ven, A

F, Bv, Ve, A

F, Bv, Ve

F, Bvs, Ven, A

F, Bv, Ven, A

F, Bv, Ven

Contact time (min.) b






No info


Residual activity c








pH range of good

activity d



(4.0 –7.0)–10.0

No info


No info

≥ 7.0

Demand load e

Inorg (N, K, Fe, Mn, S, Ar), Org,
Hard water,

Inorg (N, P, K, Cu, Mn, Zn), Org

Some reduction by hard water for Green Shield, Porous materials


Org, Some reduction by hard water

Org, hard


Corrosiveness f




No info


No info


Site usage g

Cnt, floors, GHwalls,
IrriW, NonporSrf and PorSur, tools

Cnt, floors, GHwalls, IrrgW, plants, Por PrdSur, tools

Cnt, EvpP, floors, GHwalls,
IrrigL, NonporSrf plants, PorSrf, tools


Cnt, Equip, EvpP, floors, GHwalls, tools

Cnt, benches,
Equip, floors

Equip, floors


In drain lines once diluted

Approved waste disposal h

Approved waste disposal h

Burn off in appropriate container i

Approved waste
disposal h

Approved waste

disposal h

Approved waste

disposal j

a Organisms: fungi (F), bacteria (B) vegetative (v) and spore (s) forms, viruses (V) enveloped (e) and nonenveloped (n) forms, and algae (A).

b Contact time, in minutes, is the period disinfestant should be contacting the pathogen.

c Residual activity is the time (none, minutes, hours) after application the disinfestant continues to exhibit biocidal activity.

d pH range where disinfestants have good micro-biocidal activity.

e List of solutes, suspensions and materials that place an oxidative demand on disinfestants whereby active ingredient available for biocidal activity is reduced. List includes inorganic matter [Inorg; including nitrogen (N), potassium (K), phosphorus (P), copper (Cu), iron (Fe), manganese (Mn), sulfur (S), zinc (Zn) and argon (Ar)], organic matter (Org), hard water, and porous materials.

f Corrosiveness is oxidation of metals that have a low, moderate, to high risk of development from contact with disinfestants.

g Site usage classification includes: containers (Cnt), equipment (Equip), evaporative pads (EvpP), greenhouse walls (GHwalls) irrigation lines (IrrigL), irrigation water (IrrigW), plants, nonporous (NonporSrf) and porous (PorSrf) production surfaces, and tools.

h Check product labels for specific information and contact local or state authorities to obtain contact information for appropriate disposal industries.

i An example is to pour the alcohol in a galvanized bucked that contains sand and ignite it with a match. Do not leave burning containers unattended.

j This product has acute toxicity to fish and aquatic invertebrates and has high soil mobility, so do NOT allow the product to enter groundwater by dumping it into sewers, on the ground or into a body of water.