Sanitation is critical to prevent plant diseases Part 1: Greenhouse sanitation

Learn about proper sanitation in the greenhouse and how to recognize vegetable disease symptoms.

Tomato spotted wilt virus on leaves. Photo credit: Gerald Holmes, California Polytechnic State University at San Luis Obispo,
Tomato spotted wilt virus on leaves. Photo credit: Gerald Holmes, California Polytechnic State University at San Luis Obispo,

Sanitation is one of many tactics needed for an effective disease management strategy. Sanitation refers to any practice that aims to prevent the spread of pathogens by removing diseased and asymptomatic infected tissue (not showing symptoms but in close proximity with diseased plants), as well as decontaminating tools, equipment and washing hands.

Sanitation is critical to prevent plant diseases in the greenhouse and the field. Michigan State University Extension recommends training your employees on practices that can reduce pathogen inoculum, or “seeds” of the pathogen. Consistent and effective sanitation leads to healthy plants.

Sanitation in the greenhouse

Sanitation is important year round, but prior to the beginning of a new season when the greenhouse is empty, a new opportunity to improve greenhouse sanitation awaits you. The greenhouse floor can harbor pathogens and therefore exposed soil must be avoided. An effective practice is to have concrete or gravel floors. Some other barriers are available – weed cloth or plastic – but concrete is a good, long-term investment.

Avoid accumulation of any plant debris or weeds inside and outside the greenhouse. Debris can harbor pathogens that quickly become the source of inoculum for healthy plants. Weeds can serve as alternate hosts for diseases and insects during the winter and early spring months. Weeds become the bridge for diseases and insects between two growing seasons.

Raised benches will reduce the possibility of inoculum splash from the floor to the plants on plug trays or pots on benches. Metal benches are preferred because they are less porous and therefore easy to clean. Disinfection, when done properly, can decrease the population of pathogens or nuisance organisms like algae present on various surfaces.

Initial and frequent bench sanitation is needed. Initial sanitation includes surface disinfection prior to introducing plant material into the greenhouse. Start by removing any residues or plant debris (those containing organic matter). Wash benches, walls and floors with soapy water and rinse (power wash if possible). Apply the selected disinfectant, taking into account their properties (see below). Remember, materials listed for surface disinfection can give your greenhouse a clean start, but most of them do not have residual activity. During the season, sanitation focuses on frequent collection, bag and removal of potting residue, plant debris and weeds from the greenhouse premises.

Examples of chemicals used for greenhouse sanitation

Active ingredient

Chlorine bleach

Quaternary ammonium

Hydrogen peroxide

Chlorine dioxide

Ethanol (70%)

Product (examples)

Bleach (various brands)


ZeroTol, Oxidate









Organic use approved



Oxidate is OMRI listed



Penetrate wood













Flats, pots






Walls, benches






Rinse needed






Modified from Table 1 in “Commercial Greenhouse and Nursery Production,” Purdue Extension. Surface sanitation must be done prior to vegetable transplant production begins. Remember, always read the label and follow manufacturer instructions.
*Times and method according to label specifications.
**It is best NOT to reuse containers, especially if disease was problematic in previous seasons. If reusing containers, clean flats and pots thoroughly with soapy water and scrub to eliminate organic matter (soilless media, etc.) prior to disinfection. Then submerge in a bleach solution for 10 to 30 minutes and rinse thoroughly to avoid causing damage to seed or seedlings (phytotoxicity). Change the bleach solution every two hours (maximum). 

Before entering the greenhouse, disinfect tools, boots and any other equipment. Footbaths with a disinfectant at each greenhouse entry point can prevent the introduction of pathogens from shoes or boots. Change disinfectant in footbaths daily. If you chose to use foot mats, wash and disinfect them frequently, weekly at a minimum. Alternatively, offer disposable boots to anyone entering the greenhouses.

Clean tools during use can help minimize the plant-to-plant spread of diseases caused by several bacteria and viruses. Hand-washing and sanitation can minimize pathogen spread. Provide hand-washing stations equipped with clean water and soap. Careful hand-washing is critical to minimize plant pathogen spread. For example tobacco mosaic virus (TMV) can be transmitted to tomatoes and peppers if hand-washing is not adequate after smoking cigarettes. Tobacco mosaic virus is very stable and can be present on dry tobacco in cigarettes.

Examples where sanitation can help break the disease cycle

Disease name*






Tobacco mosaic virus

Hands, tools



Squash mosaic virus

Tools, cucumber beetles, seed



Zucchini yellow mosaic virus

Tools, aphids, seed



Pepper mild mottle virus

Tools, seed



Cucumber mosaic virus

Aphids, weed hosts

Cucurbits, celery, pepper tomato, bean spinach, lettuce


Beet curly top

Weeds hosts

Beet, tomato and legume families


Tomato spotted wilt

Thrips, weeds host

Tomato, pepper, lettuce, variety of vegetables


Bacterial speck

Pseudomonas syringae pv. tomato

Seed, tools, hands, weeds


Bacterial canker

Clavibacter michiganense pv. michiganense

Weed hosts, plant debris, tools, hands


Bacterial spot

Xanthomonas campestris pv. vesicatoria

Seed, weeds hosts, tools, hands, soil & plant debris

Tomato, Pepper

*Click on the disease name and the link will direct you to additional information and symptoms pictures.

Sanitation requires detail-oriented employees. Always inspect plant material when it enters the greenhouse and prior to planting in the field. Plant material can carry diseases and insect pests, introducing them to clean greenhouse facilities or new fields. Train your employees to recognize common disease symptoms and pests. Scouting often and thoroughly is needed to identify problems as early as possible. The more eyes available to look at your vegetables plants in the greenhouse and the field, the more chances issues can be identified earlier.

The table in “Disease or disorder: How do I tell the difference? Part 2” can be useful in training your employees. Click on the disease name in the table and the link will direct you to a symptom image to help with scouting.

Plant viruses
Photo credits: TMV, ( SqMV, H. Lecoq, INRA Station de Pathologie ( Bacterial spot, Clemson University (, TSWV, Bacterial canker, and bacterial speck, Gerald Holmes (

Greenhouse sanitation practices summary

  • Disinfect surfaces such as greenhouse benches, potting stations, etc. before transplant production season.
  • Remove plant debris by collecting, bagging and removing.
  • Remove infected plants as soon as symptoms appear by collecting, bagging and removing from greenhouse premises.
  • Disinfect knives, shears and other harvesting tools.
  • Frequent hand-washing with clean water and soap.
  • Brush soil particles off from shoes when moving in between greenhouses (floor mats, baths, brushes or boot covers are handy).

For Part 2 of this two-part series, see “Sanitation is critical to prevent plant diseases Part 2: Field sanitation.”

Spanish versions of these article series are available for download:
Part 1 – Saneamiento en el invernadero: qué se debe hacer para evitar la transmission de enfermedades en hortalizas
Part 2 – Saneamiento en el campo: qué se debe hacer para evitar la transmission de enfermedades en hortalizas

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