Pest or Pathogen: Getting the Diagnosis Right

By Sally Nex
Published: March 12, 2019 | Last updated: April 23, 2021 03:05:53
Key Takeaways

As in humans, the symptoms of one plant problem can look a lot like another. Here are a few tips on how to make the right diagnosis and how to avoid issues altogether.

As any doctor will tell you, the symptoms of one disease can look a lot like another. A patient complaining of headaches could be suffering from stress at work, poor eyesight, migraines, or a brain tumor. An aching knee can be caused by overdoing it at the gym, tendonitis, arthritis, or brittle bone disease. It’s the same when you’re trying to figure out what’s wrong with your plants. Yellowing leaves can be a normal sign of aging or something more sinister like iron deficiency.


Without knowing what’s wrong, you won’t know what to do to put it right. Worse yet, you might administer the wrong medicine entirely. To make the right diagnosis, growers need to dig a little deeper, ask the right questions, and weigh all sorts of clues. It’s a sleuthing exercise Columbo would be proud of.

Making the Right Diagnosis

Plant Diseases can be fungal, bacterial, or viral, and they can affect leaves, stems, or roots. Pests attack all parts of a plant, eating away tissue or tunneling holes that then develop secondary fungal infections. Then, there are cultural problems, the plant equivalent of malnutrition or heatstroke. These physiological ailments caused by less-than-ideal growing conditions.


Regular patrols of your plants allow you to spot problems quickly, so spend a few minutes every day just assessing what shape your plants are in. That way you’ll notice every hole, puckered shoot tip, or browning leaf the moment it appears, and you can swing into action before a pathogen takes hold. Even the slightest delay can dramatically worsen the problem you’re dealing with; aphids, for example, reproduce so fast they quintuple their numbers every 24 hours, while blight can destroy a previously healthy tomato crop in as little as 10 days.

Deciding which you’re dealing with is a matter of detective work. Arm yourself with a good reference book on pests and diseases before you start so you have all the information you need at your fingertips. The American Horticultural Society’s Pests and Diseases is among the best. It’s a complete guide to every kind of plant ailment with advice on prevention and treatment, as well as identification.

Be methodical in your inspections and try to keep an open mind. It may not be the obvious sign that tells you what the problem is. It could be something much more minor and difficult to spot, so look closely. Turn the leaves up and look at the undersides and inspect tender new growth like shoot tips where pests like to gather. Take note of cultural conditions such as weather and when the plants were last watered. Also, remember many pests and diseases stick to just one family of plants. For example, stunted growth in brassicas like cabbage and cauliflower could be caused by clubroot, a nasty fungal disease that only attacks this group of plants. However, if your cucumbers are also stunted, the cause is more likely to be a mosaic virus.


Gradually, you narrow down the field to just a few possibilities and, eventually, a firm diagnosis. Then, treatment can begin.

Prevention is Better Than Curing

They say an ounce of prevention is better than a pound of cure, and that is so true with plants. By the time you’ve spotted signs of a pathogen, some damage is already done. So, grow disease-resistant varieties where you can, and pay attention to hygiene. Take the few seconds to disinfect pruning shears between plants and spend half a day cleaning the greenhouse properly at the end of the season to evict overwintering pests; these small tasks make all the difference in keeping your plants healthy.


Just as important is growing your plants well. Keep them growing as vigorously as you can by feeding and mulching regularly and providing just the right amount of water, light, and humidity, and they’ll shrug off pest and disease attacks with ease.

Five Easily Confused Plant Problems

Red Spider Mite or Magnesium Deficiency?

Imagine a greenhouse full of cucumbers whose leaves gradually begin to turn yellow. At a glance, you could easily diagnose the problem as a lack of magnesium, an essential mineral that plants need to produce healthy leaves and photosynthesize. However, look closer and you may notice tiny specks clustering under the leaves and fine web-like threads. These are the tell-tale signs of the red spider mite, a tiny but voracious sap-sucker that attacks most greenhouse crops from mid to late summer.

Telling Them Apart

Red spider mites tend to cause finely mottled leaves, while a magnesium deficiency causes leaves to be blotchier. Also, unlike with red spider mites, the veins of magnesium-deficient leaves stay green. To make sure what you’re dealing with, turn the leaves over. Red spider mites appear as tiny yellowish-green specks on the undersides. As infections build, they also produce a fine silk webbing much like cobwebs.


Red Spider Mite: Keep numbers down by releasing a biological control such as the predatory mite Phytoseiulus persimilis, or spray with insecticidal soap.

Magnesium Deficiency: Spray leaves with a foliar feed made of a solution of Epsom salts two or three times every two weeks.

Blight or Drought Stress?

Late blight (Phytopthora infestans) is a devastating fungal infection whose name strikes dread into any vegetable cultivator growing in a mild, damp climate. Once rain washes late blight spores onto your plants, they spread voraciously, reducing potatoes and tomatoes to rotten mush within a few weeks. Alarm bells should start ringing as soon as you spot tell-tale brown patches on the leaves. However, brown spots also turn up on tomato and potato leaves after prolonged spells of drought. Plants usually recover from drought, but blight is always fatal.

Telling Them Apart

At first glance, the browning caused by drought damage and the lesions of late blight both look quite similar. But look closer and you’ll find the brown patches on drought-stressed leaves are just dry, dead leaf. Blight lesions, by contrast, are fuzzy with spores. They also sometimes appear on the stem.


Blight: Remove affected foliage to slow the spread. Pick off tomato fruits straight away. For potatoes in which the infection covers about a third of the plant, cut away the top growth and harvest early.

Drought damage: Prune out affected growth and the plant should recover. Also take the steps to improve water delivery. A compost mulch over damp soil locks in water, and irrigation channels alongside each row make sure none is lost to evaporation.

Onion Fly or Onion White Rot?

You’ll probably never see an onion fly. It’s small, grey, and unremarkable. You’ll notice the damage its larvae cause, though. They work out of sight, munching through onion, shallot, and garlic bulbs to reduce entire beds to soft, rotten mush just as they reach their peak. However, onions can also rot mid-season from another, more sinister cause. Onion white rot is one of the most persistent fungal diseases. It produces pinhead-sized black resting bodies known as sclerotia, which survive in the soil for 15 years or more, reinfesting and ruining each successive crop.

Telling them apart:

The first symptoms are superficially the same: leaves wilt and turn brown and the top of the bulb begins to rot. Dig up an affected bulb, though, and look closely. White rot begins at the base of the bulb, spreading upwards from the roots. Onion fly maggots, however, start at the top and work down. You’ll sometimes also see them wriggling in the top of the bulb.


Onion Fly: Lift the damaged bulbs and burn them to kill the maggots. Rotate crops into clean ground each year, and plant under mesh to prevent adults laying their eggs.

Onion White Rot: White rot is almost impossible to get rid of once established, so prevent it by buying seed and sets from reliable source. Good garden hygiene helps too. If you have infested ground, grow onions in containers instead.

Slug Damage or Damping Off?

A gardener never tires of that magical moment when new seedlings unfurl from the compost for the first time. So, when your seed trays stay resolutely empty or produce just straggly patches of weedy, sorry-looking shoots, it hits you right where it hurts. Your local slug population may have discovered there’s a fine new meal to be had, munching away your new shoots the moment they poked their heads above ground. Or your babies may have succumbed to damping off, a vicious fungal pathogen capable of destroying a tray of healthy seedlings within hours.

Telling them apart:

Slugs leave a tell-tale trail of slime wherever they go, so this is your giveaway for a slimy mollusc attack. Damping off, on the other hand, is a fungal disease. When it attacks seedlings after they emerge, you’ll see their remains on the surface, often covered in white, fluffy mold. Pre-emergence damping off happens below compost level, so your seedlings simply fail to come up.


Slug Damage: Check your seed trays daily, especially when it’s damp, to search out and destroy lurking slugs. Wildlife-friendly ferrous phosphate slug pellets also help.

Damping Off: Use sterilized seed compost and clean containers, and sow seeds sparingly to allow lots of air circulation between the resulting seedlings. Don’t water with rainwater, which can carry disease, and keep trays damp but not soggy.

Downy Mildew or Powdery Mildew?

These fungal diseases are both bad news, turning up as fluffy fungal growth on foliage and fruit that spread rapidly through your plants and turn your crops to mush. That’s where the similarity ends, though. Downy mildew is a damp-conditions fungus. It likes the cool, wet conditions of spring and autumn, and it turns grapes, lettuces, peas, and spinach to white, moldy rot. Powdery mildew prefers dry conditions. It turns up in the heat of summer on zucchini, squash, and cucumbers, weakening plants and bringing the harvest to a sudden, early stop.

Telling them apart:

The climate and time of year tell you which of these two nasties you’re most likely dealing with. They look different too. Powdery mildew is obvious, appearing on the upper surfaces of leaves as a dusting of white. Downy mildew is more difficult to diagnose. It can cause leaves to develop pale yellow or green blotches. Turn them over and you’ll find a corresponding patch of fluffy fungal growth.


Downy Mildew: Pick off affected leaves to slow the spread. In greenhouses, open vents whenever possible and water at the feet of plants to avoid wetting their leaves.

Powdery Mildew: Keep plants well-watered, as dry roots make them more susceptible to the disease. Pick off infected leaves to slow the spread. Also, look for resistant varieties to grow next year.

When you first discover your sick plants, diseases and pest attacks can seem like mysterious disasters. Don’t panic, though. Take time to methodically work through the symptoms and figure out exactly what’s wrong. Once you know the ailment, like any good doctor, you can prescribe the right medicine. With the right prescription and a little luck, your plants should bounce back and make a full recovery.


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Written by Sally Nex

Profile Picture of Sally Nex
Sally Nex is a gardener and garden writer living in Somerset in southwest England and has been growing fruit, vegetables and herbs to feed her family year-round for more than 20 years. Her articles and advice have appeared in national gardening magazines, newspapers and websites.

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