Sources, spread and survival of pathogens, pests and weeds in ornamental crops

Learn about the sources, spread and survival of common pathogen, pest and weed problems by cropping area and how to control them.

Back to: Guidelines on nursery hygiene for outdoor and protected ornamental crops

A checklist of the common ways pests, pathogens and weeds arrive and spread on a nursery, arranged by inspection area, is provided in Table 1.

Many pest and disease organisms have more than one method of spread, such as via air currents, on crop debris or by direct contact. This makes them difficult to control, but attempts should still be made. Preventing or delaying introductions of pests, pathogens, and weeds onto crops reduces the risk of damaging populations building up.

Information on the survival of selected pests, pathogens and weeds is summarised in Table 2. Many can survive for months or even years in the absence of a crop.

Once used, containers and trays need to be cleaned and treated with disinfectant before reuse to kill pathogens, pests and weed seeds, and covered after treatment

Image © ADAS Horticulture

Dirty floor or bench coverings can be a source of root-infecting pathogens, especially Fusarium, Pythium, Phytophthora, Rhizoctonia and Thielaviopsis, and some pests

Image © AHDB

Table 1. A checklist of the common pathogens, pests and weeds in ornamental crop production, arranged by nursery area/input, with outline control measures


Type of problem spread this way

Control measures

Glasshouse structure

Viruses, some fungal pathogens, overwintering pests, e.g. two-spotted spider mite

Clean and disinfect. Control spider mites on the crop before they enter diapause and overwinter

Benches and matting

Some pathogens (especially root-infecting water moulds/oomycetes such as Pythium and Fusarium). Some pests with ground-dwelling life stages, e.g. thrips, sciarid and shore flies, leaf miner

Clean and disinfect. Renew old matting. Remove dead or dying plants and debris. If appropriate, apply biological control agents against insects and mites, e.g. ground-dwelling predatory mites, beetles or nematodes and bioprotectants for disease control


Some pathogens in debris and dust; various pests (as for benches and matting), also slugs, snails, woodlice and vine weevils; insects and nematodes on plant debris or feeding on algal growths; moss and  liverwort

Clean the floor, control algal growth, mosses, and liverwort. Renew covering. Level hollows to eliminate puddles. Apply biological control agents and bioprotectants if appropriate, as for benches and matting

Machinery and equipment

Fungal and oomycete spores, bacteria, viruses, weed seeds, pests, e.g. thrips and leaf miner pupae

Regularly clean seeders, transplanters (especially fingers on machines), potting machines, secateurs, knives etc. Keep work areas clean

On wheels of fork lift trucks, soles of shoes, etc.

Oomycetes, root-infecting pathogens, viruses, pests with a life cycle stage on the ground e.g. thrips and leaf miner pupae

Allocate specific vehicles to high-risk areas. Clean vehicles regularly. Place disinfectant-soaked matting across entrances to high-health status areas

Cropping aspects

Type of problem spread this way

Control measures


Some fungal and bacterial pathogens, less commonly viruses; contaminating weed seeds

Use certified, high-quality seed. Request seed treatment where there is a known risk of a seedborne pathogen. Seed testing

Incoming cuttings and young plants

Some fungal, bacterial and viruses; some pests, e.g. thrips, leaf miner, whitefly, nematodes and vine weevil larvae (in plugs or liners)

Inspect and quarantine incoming stock; use sticky traps. Use virus-tested stock. Use stock indexed for vascular pathogens. Avoid placing plants on the ground or a dirty work surface. Apply biological control agents or bioprotectants if required

New containers

Pathogens, weed seed

Regularly brush or vacuum pathways and areas around potting machines. Store under cover or shrink-wrapped if outside. Store old pots separately from new ones

Reused containers

Some pathogens, particularly their resting stages (e.g. Thielaviopsis, cause of pansy black root rot); weeds (e.g. bittercress around edges of old containers); slugs and snails under trays, pests on plant debris, e.g. thrips, leaf miner, nematodes, spider mite

Clean and disinfect before reuse (e.g. high-pressure wash the trays using water containing a disinfectant). Note: disinfectants alone may not kill weed seeds; cleaning first is essential

Growing media, soil and dust

Occasional pathogens, weed seed (especially in dust), some pests

Protect growing media from dust and run-off water. Cover bunkers and part-used or damaged bags. Agree growing media specification and keep samples


Some fungal pathogens (especially oomycetes), bacteria and weed seed

Cover storage tanks. Routinely test recycled and stored water, and storage tanks, for plant pathogens. Treat recycled water. Check water treatment equipment is working correctly. Clean and disinfect irrigation lines. Avoid irrigating with contaminated water, especially young plants. Do not drop hoses on dirty ground. Avoid water splash. Keep reservoir banks free of weeds and plant debris

Crop covers (e.g. fleece)

Some pathogens and pests, in particular resting spores of pathogens or pupae

Dispose of contaminated crop covers and only reuse crop covers in low-risk situations

Growing and standing areas

Weeds, pathogens, pests. On sloping sites, run-off water can spread root pathogens to plants lower down the slope (especially Phytophthora)

Sweep floors and benches regularly, disinfect as necessary. Ensure standing areas are adequately drained. Ensure ground cover material is in good repair and covers all the growing area up to path edges. Replace capillary matting as necessary. Skim sand beds. Check uniformity and distribution of irrigation. Remove diseased and infested plants promptly. Put IPM strategies in place on new crops promptly. Seek to devise production routes to minimise old crops contaminating new crops. Do not set down new crops in spaces between old crops

Insect movement

Flying pests, e.g. aphid, adult thrips, leaf miner, leafhopper, whitefly, sciarid and shore flies. Crawling pests, e.g. slugs, snails, adult vine weevil. Some fungi and viruses carried within insects (e.g. Pythium and Fusarium with sciarid flies, tomato spotted wilt virus with western flower thrips)

Use sticky traps to monitor insect levels. If appropriate, use roller traps for mass trapping of pests. Monitor indicator plants. Control pests that can cause crop damage or transmit disease

Air currents

Small pests, e.g. thrips, some fungal pathogens, wind-blown weed seed

Use sticky traps to monitor for thrips and other pests. Consider screening vents with insect-proof mesh, or use sticky traps under vents or next to doors. Use windbreaks to reduce weed seed blown in from surrounding fields

Contact between plants

Botrytis, crawling pests, e.g. spider mite, aphid, thrips larvae

Remove affected plants. Give adequate plant spacing (unless using biological control agents, e.g. Amblyseius species and Phytoseiulus persimilis, which need plants to be touching)

Waste plants and crop debris

Some fungal pathogens and pests, e.g. western flower thrips (WFT) on unmarketable flowering plants

Place unmarketable plants and debris in covered skips or other covered containers. Cover any heaps of plant waste near the nursery. If composting in open heaps, locate them at least 10 m away from production areas

Non-cropping aspects

Type of problem spread this way

Control measures

Non-cropped areas

Pests on weeds, e.g. whitefly and leaf miner on chickweed and sowthistle under benches or around edges of glasshouse. Occasional fungal pathogens on weeds (e.g. rusts, botrytis). Weed seeds

Control weeds in and around cropping areas and outside glasshouses, especially next to stored growing media, water tanks and reservoirs. Use vegetation-free strips or closely mown grass around houses and production areas. Do not allow rubbish to accumulate near growing media mixing areas

Dispatch areas

Pathogens, pests and weed seed on trolley shelves and wheels of trolleys, forklift trucks and lorries

Clean floor regularly. Clean and disinfect trolleys before reuse. Devise routes to avoid cross-contamination between dispatch and production areas

Staff and visitors

Some fungal and viral pathogens and pests, e.g. powdery mildew, spider mite and thrips on clothing

Ensure staff are trained in and follow nursery hygiene procedures; display the nursery hygiene rules and practices as a reminder. Ensure visitors and contractors working on-site report to reception and follow the nursery hygiene policy. Avoid staff movement from infected/infested areas to ‘clean’ areas. Use protective clothing, gloves and hand-sanitisers in high health status areas. Use disinfectant foot dips. Wash hands regularly. Do not allow staff to raise their own plants on site unless a risk assessment indicates minimal risk

Table 2. Persistence of some key pathogens, pests and weeds on structures or in the soil or growing media




Black root rot dispersal spores

4–5 years in root tissue

May occur in nursery sweepings. Capable of prolonged saprophytic survival in soil

Botrytis cinerea dispersal spores

Weeks to around 1 year

Many environmental factors reduce survival (e.g. sunlight, frequent wetting and drying). Ability to infect plants may decline more rapidly than ability to germinate

Downy mildew dispersal spores


Information relates to Peronospora parasitica on leaves under typical field conditions. Spores desiccate. Longer-lived resting spores can be formed

Fusarium oxysporum resting spores


Cyclamen fusarium wilt tends to reoccur in a nursery after a severe outbreak, possibly due to persistence between crops on matting or benches. Long-lived in soil

Powdery mildew dispersal spores


Washing a glasshouse with water can trigger spore germination and reduce survival

Pythium resting spores


Will survive drying on a range of surfaces

Phytophthora dispersal spores


Varies with species. Some species, e.g. P. ramorum can be dispersed into the air, others, e.g. P. cactorum, are shed into water

Phytophthora resting spores

Months to years

Varies with species, but generally several years

Rhizoctonia solani resting structures


Capable of prolonged saprophytic survival in soil

Sclerotinia sclerotiorum resting structures

6–8 years

Contans WG is available for biological control of soilborne resting structures; also consider soil disinfestation or growing out of the soil if a serious problem

Soft rot bacteria, e.g. Pectobacterium carotovorum


Commonly occurs in soil and water, so re-infestation may readily occur

Tomato mosaic virus (ToMV)


Can survive for years in plant debris





Weeks to months

Most species do not produce eggs. Aphids will only survive on host plant material, e.g. crop plants, weeds or leaf debris

Caterpillar and moth pupae


Some species pupate in soil or growing media and can overwinter. Other species, e.g. carnation tortrix can overwinter as larvae in rolled up leaves of host plants

Glasshouse whitefly

Weeks to months

Will only survive on host plants, weeds or leaf debris. Can overwinter in glasshouses and on weeds outdoors in mild winters

Leaf miner pupae

Weeks to months

Liriomyza species can survive for several months in soil or growing media, depending on species and temperature. Native Chromatomyia species pupate in the leaf and can survive in leaf debris

Two-spotted spider mite


Can overwinter in glasshouse structure and equipment

Vine weevil


Larvae and pupae (both in soil or growing media) and adults (in sheltered refuges) can be found all year round in glasshouses but usually overwinter as larvae and pupate and emerge as adults in spring

Western flower thrips (WFT)


Depending on temperature and moisture, may overwinter as adults, larvae or pupae, on plants, plant debris, weeds or in soil




Annual meadow grass

> 5 years



Many years

Most germinate within a year, but a small percentage can remain dormant for 60+ years

Common sorrel

> 5 years

Occasionally problematic in growing media


> 5 years

Most germinate within a year, but a few can remain viable for longer

Hairy bittercress

> 5 years


Liverwort spores

Around 1 year

Spores kept at room temperature were 100% viable after a year, 50% after 14 months and failed to germinate totally after 17 months

Useful links

Read the AHDB crop walker guides for bedding and pot plants, cut flowers and hardy nursery stock to familiarise yourself with the range of issues encountered in the production of ornamentals.

Crop Walkers' Guide: Bedding and pot plants

Crop Walkers' Guide: Cut flowers

Crop Walkers' Guide: Hardy Nursery Stock


The content for these web pages were originally authored for AHDB by:

Author(s) – Dave Kaye and Erika Wedgwood. ADAS Horticulture.

Original author(s) – Tim O’Neill, Wayne Brough, John Atwood and Jude Bennison, ADAS.

Webpage content correct as of June 2021.

Got a question? Ask a member of the team: