By Ruth Vaughan

In intensive horticulture, soil borne diseases cause yield and quality loss, and if left unchecked can result in complete project failure, as we have seen happen many times. All soils, unless completely dead, have a large and diverse microbial population, some good and some bad.

The trick is to keep the soils in balance so as to completely avoid a takeover by bad microbial populations that damage crops and hinder their growth. Some of the ways a healthy soil balance can be achieved are discussed below.

Horticulture Soil Borne diseases

All soils, unless completely dead, have a large and diverse microbial population, some good and some bad

Pre-emergence damping off

Pre-emergence damping off happens when seeds rot in the ground and do not germinate. The condition may occur right at the beginning when seeds are planted and can easily be mistaken for bad seed quality. Pre-emergence damping off occurs when conditions are poor: too cold, too hot, too wet, too dry, poor drainage, undecayed organic matter, high soil salts or compacted soil.

Post-emergence damping off

If the seeds germinate and grow out of the soil, then suddenly die off, this is called post-emergence damping off. Stressed plants or weak plants are attacked leaving their roots below the soil and their tender stems susceptible to disease attacks and sudden ‘fall over’ death. This can also be caused by overfeeding plants with nitrogen from too much manure or fertilizer, causing very soft leggy growth.

Damping off diseases are caused by a number of funguses, like Pythium, Fusarium, Rhizoctonia and Phytophthora. It is always a good idea before you embark on a costly venture to have a pathology check on your soil before planting, to make sure that these pathogens are not present in the soil.

Vascular wilts

Other diseases that are the bain of many farmers are the vascular wilts. They can come in at any time during the crop growth cycle when plants are under stress and attack the crops through the roots. Unfortunately, very often, they come in just before harvest, after a farmer has invested a lot of resources. Plant wilting and discoloration of the vascular system inside the stems characterize vascular wilts.

Evidence may be seen through a gradual loss of vigor in the plant, followed by wilting starting at the growing point; yellowing; twig dieback; leaf, flower, bud and fruit drop and eventual plant death. Vascular wilts can be fungal or bacterial. Bacterial wilts include Ralstonia, Erwinia, Curtobacterium, Clavibacter, Pseudomonas and Xanthomonas.

Vascular wilts are characterized by plant wilting and discoloration of the vascular system inside the stems.

Bacteria breed up in the stem, blocking vascular tissue and preventing uptake of water and nutrients. They penetrate easily and quickly kill the crop. Vascular wilts can be locally tested by cutting and placing stems in a clean glass of water. If positive, you will see a cloudy bacterial stream oozing out of the bottom of the stem.

Plants already infected cannot be cured and the effects can be catastrophic, with the only possible remedy being the complete removal and burning of the plants and the soil that they are growing in. Similar to damping off, fungal bacterial wilts are caused by soil-borne fungi and include Verticillium, Fusarium, Rhizoctonia, Pythium and others.

If fungal vascular wilts are caught early, plants may be saved by using a systemic fungicide, although some fungal wilts are incurable (always check the label and make sure the fungicide is PCBP-approved for your crop and adhere to the post-harvest interval recommendations.)

Generally fungal wilts cause a discoloration inside the vascular bundle and they can all look pretty similar. It is important to send a plant sample for pathology to identify the causal agent and problem for the treatment possibilities of the current crop, but also forecast planning the next crop. Often a plant may have a disease complex, which consists of more than one pathogen. These are very hard to treat.

How to prevent soil-borne diseases

Crop rotation – this is very important, some diseases affect one plant type and not the other, if you rotate your crop, the pathogens do not build up in the soil. Even roses can have a ‘break’ crop; for example, Calientes mustard seed is a great short-term break crop that will rejuvenate your soil big time. Seeds are readily available in Kenya – search

Soil health – make sure that your soil has a good structure and cation balance, with plenty of well-rotted compost. Send your soil to the laboratory for a complete soil analysis with lime/gypsum recommendations before planting – this will reward you with a good healthy productive crop for many years to come.

Soil moisture control – very wet soils really, really do cause disease. Some fungal pathogens remain dormant in the soil until the soil becomes too wet when you over irrigate. Wet soil is anaerobic (has no oxygen in it), and many pathogens like anaerobic conditions, so you get more of a bad pathogen build-up rather than the good. The plant roots need oxygen to take up water and nutrients. They can’t do this in wet soil and become weak and prone to disease. Dry soil is just as bad, the plants get stressed and weak and start to wilt, which causes breakages in the roots and stems and entry points for pathogens. ‘Catch-up watering’, also known as flooding dry soil, is the biggest cause of late onset vascular wilts. Striking a balance is key and you must dig down to the roots to really look at the soil moisture and understand its state. Smell the soil!

Avoid soil compaction in the root zone – dig some soil pits in your fields to look at the soil profile and root structure. Compaction limits root volume causing stressed weak plants that are susceptible to disease. It is much better to build raised beds to improve aeration and drainage in the soil.

Nematodes – are not a soil borne disease, however, pathogenic nematodes feed on plant roots and weaken the plants as well as creating entry points for soil-borne diseases. Very often nematodes are associated with vascular wilts and damping off. It is important to check your soil and treat the nematodes if they are there. The combination of disease spores and bad nematodes in the soil will give any farmer endless problems.

Salinity – high sodium and high electrical conductivity (EC) causes problems with soil and root structure and water infiltration, which is a major cause of damping off diseases. A complete soil analysis will let you know what salts are in the soil. Very often the sodium will come from the irrigation water, so it’s always a good idea to have that checked too.

Soil pH – should be optimum as very high or low pH can encourage different diseases. High nitrogen – over-application of manure, compost and fertilizer at bed preparation and planting is one of the main causes of damping off disease. Too much of a good thing can be bad. Check the soil and follow the guidelines.

Soil temperatures – some soil diseases take hold at very high or low temperatures. Over-watering can reduce soil temperatures and mulching can improve them. A happy, diverse and active soil can ‘warm’ itself up.

Beneficial micro-organisms – having a lot more of the good than the bad micro-organisms in the soil can make a huge difference to disease pressure. The beneficial microbes work in many varied ways, feeding and out-competing the bad microbes by strangling them and recycling plant nutrients to make them more available, thus creating a stronger healthier plant. Beneficial microbes are easily available and spending money on these at the planting stage will save you chemical bills and pesticide residue problems later on.

If you have a problem with persistent plant diseases or want to get your project off to a good, sustainable, disease and risk-free start, contact our agronomists on [email protected] and see what we can do to help you!

Till next time,

Happy farming!


About Ruth

Ruth vaughan cropnuts


Ruth Vaughan is the Technical Director at Crop Nutrition Laboratory Services Ltd. (CROPNUTS). Ruth is also a contributing author to Kenya’s leading horticulture magazines such as the HortFresh JournalHortiNews and Floriculture. Ruth is a great believer in soil health, organic matter, biochar and carbon sequestration as a way to alleviate climate change and increase food security. Loves visiting farmers and seeing all the different farming methods

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