Root Rot Detection and Treatment for Plants

Not all plant diseases and infections are visible when you look at the surface. Root rot, for example, is caused by a bacteria or mold that begins killing your plants at the roots and under the soil, then can spread through the plant into the stem if left untreated. The signs of root rot are similar to overwatering, underwatering, and heat exposure, so if you didn’t know it was root rot, it could be too late by the time you discover it. That’s why we created this guide to detecting and treating root rot for your plants.

First, you’ll learn what root rot is, then we'll go into treating it, since that is most important. From there, you’ll learn the causes, ways to detect and identify root rot, as well as some tips on preventing it from happening.

Root and stem rot is the general term for the plant disease caused by a population of bacteria, fungi including mold, or a combination of both increasing in the soil and infecting the plants rooted in that soil. All root types can be affected by root rot including taproots and fibrous.

The bacteria and mold begins rotting away the roots preventing them from being able to absorb water and nutrients. Without water and nutrients, the plant begins to starve and dehydrate leading to death. Without early detection and treatment, root rot will kill the affected plant and spread throughout your home or garden. This disease can affect houseplants in pots as well as landscaping plants.

The good news is that root rot is one of the easiest plant health issues to treat, and in most cases it only takes less than 10 minutes to do.

To treat root rot in your plants follow these five steps.

1. Carefully remove the impacted plant and rinse the root system clean from any dirt, soil, or potting mix so you can examine all of the roots.

2. Separate any roots that are mushy, discolored in browns, and smell musky like mildew as these are the “rotting roots”.

3. Trim any rotting or dead roots with sharp, sanitized shears. 

   1. If it is discolored, smells or feels squishy, trim it off.

4. Treat the roots and the pot the plant was in if it is a houseplant with a hydrogen peroxide solution (3 parts water to 1 part peroxide) or plant-safe fungicide to make sure all bacteria, mold, and other contaminants are washed away. 

   1. Follow the manufacturers instructions for how often to use, usually every 5 - 6 days, during an active infection.

5. Re-pot in a new well-draining potting mix like our Dirt Bag, ensuring the pot has holes in the bottom for proper drainage.

Root rot is easy to treat and if you get all the rooting rots off of the plant, change the potting mix or soil, and treat the container the plant is in (if it is a potted plant), it likely will be gone. Now that you know how to get rid of root rot, here’s the cause, ways to detect it, and some tips on preventing it.

The cause of root rot is anything that provides an environment for bacteria and mold to grow include:

• Too much moisture

• A lack of drainage

• Not enough oxygen causing “anaerobic” soil (a lack of oxygen)

• Exposure to specific bacterias and mold

• Contaminated tools, soil, decorative items, or potting mix

• Insect and pest infestations if they damage the roots or brought the bacteria and mold in

Overwatering, soil with poor drainage (or with poor aeration), and potting mix that is already contaminated by fungi can all cause root rot. Your potting mix or soil is similar to your gut microbiome, where you have some resident bacteria or fungi naturally that keep each other's populations in check. This creates a delicate balance and helps plants grow by giving off byproducts like nitrogen that are beneficial.

By overwatering, or having soil that has poor drainage so it retains water, a dark, soggy, poorly oxygenated environment is created that promotes the increase in the population of bacteria and fungi that competes with the good bacterias in the potting mix. 

With an increase in population and the bad bacterias winning, the soil no longer provides enough nutrients, so the bacteria and fungi will begin eating away at your plants starting with the roots. Bacterias can get into the potting mix naturally from overwatering, be introduced via contaminated soil or potting mix, and by non-sterilized or affected shears, rakes or forks, and spades when you are doing your normal plant care like trimming and aerating.

The direct causes of root rot include anaerobic bacteria like Pseudomonas, and fungi that thrive in waterlogged environments leading to mold growth like Fusarium, Rhizoctonia, Phytophthora,Pythium, and Dematophora necatrix, which causes white root rot. 

Soil or things used for landscaping and decoration like rocks or wood, might contain resident fungi which can cause root rot. This is why plants from outside should be repotted in fresh potting mix and treated with a plant safe fungicide before adding them. And if you want to add decorations like a cute log in your terrarium, carefully inspect and clean it before introducing it to the eco-system. 

Root rot can be detected by:

• Smelling a musky and mildew odor coming from the soil or potting mix

• Finding squishy root systems

• Discolored roots with rotting colors including brown, yellow, and tan (anything not natural for the plant and that is decaying)

• Wilting leaves and stems

• Discolored leaves and stems starting with yellow and turning brown when they die

• Drooping leaves with moist soil or potting mix

Without access to oxygen due to soggy soil, your plant will start to rot and die while bacteria and fungi will thrive, leading to a cascade of visible problems that can help you detect root rot. While called root rot, the signs of this plant disease are not exclusive to the roots because the bacteria or fungi will travel up the root system into the plant's vascular system (the xylem) to infect the whole. When this happens the plant begins to rot from the inside out.

Yellowing leaves indicate the soil is likely overwatered which creates an environment that suffocates roots and promotes bacterial and fungal growth. Gray, brown, black, white, or even bright red spots on the leaves, stems or roots are visible signs of a fungal or bacterial infection within the plant from root rot. You might also see other fungal structures show up in your pot, like mushrooms. 

Yellow or red spots on the leaves can also indicate nutritional deficiency which might be caused by root rot. Brown mushy roots is a telltale sign of root rot as most types of roots should be white, firm, and similar in texture. 

Pro-tip: Brown mushy roots are not always root rot, if you are switching from water propagation to potting mix your plant will switch the type of root it grows, and the water roots will turn brown and mushy as they start to degrade. If you are seeing two different types of roots, and there is no foul odor, it’s likely your plant is likely in transition and does not have root rot. 

Plant stems should feel firm, if they feel mushy it is a sign of a problem. Mushy or slimy feeling roots are also a sign of degradation and should be removed with sanitized shears. 

Drooping leaves are usually a sign of underwatering, but if you have drooping leaves even with moist soil that means the roots are not functioning properly and absorbing water. A lack of strength in the stems or base with slowed or stunted growth is another sign the root system is not functioning properly or absent due to having begun to rot as the nutrients can no longer provide the plant with the strength it needs to stand.

Mold or sour/rotten egg smells from the soil are a sign of root rot as the anaerobic bacteria will produce hydrogen sulfide (H2S) gas as a byproduct of their digestive system in order to gain energy. This gas causes a rotten egg smell due to the sulfur. 

Preventing root rot is as simple as:

• Keeping the dirt your plant grows in aerated and well draining

• Cleaning and disinfecting all tools, decor items, and other materials that your plants will be exposed to

• Checking that the dirt, potting mix, or soil is moist but not waterlogged once a week.

• Disinfecting and using a plant safe fungicide on the container or pot when you change your potting mix.

• Checking and trimming any dying or unhealthy roots when you repot or replant your plants.

Preventing root rot is easy by not overwatering your plants and choosing a well-aerated potting mix with organic material like peat moss. Periodically inspect your pot’s drainage holes to ensure they’re not blocked so you do not create an environment where bacteria and fungi can thrive. Do not add rocks inside your pots at the bottom, as this can block drainage holes and create hidden nooks where water can accumulate instead of drain. 

Plant-safe fungicide is not just for active root rot, but can also be used as a preventative to protect against fungus, mold, mildew, and rot by applying to the soil or plant leaves once every 2-3 weeks. For a cheaper, more natural preventative, you can also use diluted hydrogen peroxide (H2O2) on the soil, as it will break down into water and an oxygen free radical that helps aerate the soil and discourage anaerobic bacterial growth. Just make sure your plants can handle this by reading about them first, or contacting the store you purchased them from.

Pro-tip: When adding any chemical whether it’s fungicide or fertilizer to your potting mix, make sure to dilute it properly or you risk causing chemical burns. 

Use sanitized tools, including your gardening hose, spade and shears, as fungi or bacteria can live on these surfaces and transfer into the soil to infect your plants. Before and after use you can use a 10% bleach solution on your tools, soap and water, or alcohol to sanitize. 

Landscaping items like rocks or logs should also be sanitized before being added to your plants environment. If you don’t know where it’s been, sanitize, inspect, then place. 

New plants should be inspected carefully, with a period of isolation of at least a week when they come into your home or garden before they are grouped. This helps to ensure they are not ill with root rot or contaminated by other diseases or pests. All new plants should also be repotted in fresh potting mix giving you the opportunity to inspect all the roots and any unknowns from lurking in the soil before they can affect other plants once grouped. You can reuse the pot it came in as long as it has been sanitized first. 

Pro-tip: When repotting, do not compact the soil as this reduces the air pockets in the soil. Instead, do a layer of potting mix, then add your plant, then fill the rest of the pot while gently shaking/shimmying the pot to get the soil to settle. 

Last, never reuse water that has been used to water your houseplants or from drainage, as fungi like to grow in stagnant water. Only water with fresh water each time. 

Root rot is one of the easiest plant diseases to treat, and preventing it is a matter of not overwatering your plants, not introducing infected items or materials, and making sure water can drain out. If you see root rot, don’t panic, follow the instructions above and you can likely save your plant if you detect it early enough.