Subtropical Fruit Crops Research & Education
University of California
Subtropical Fruit Crops Research & Education

Posts Tagged: cinnamomi

Drought or Root Rot? - 12 Steps

We recently had a series of workshops on Avocado Root Rot and ways to manage it.  A common question was how to figure out whether the tree was diseased with Phytophthora cinnamomi  or just stressed from lack of water.  Drought is also compounded and confused by salt accumulation, which is a reflection of how water is being managed. It might be the right amount, but not timed correctly.  Too much at one time means the water goes beyond the shallow root system, too little at an irrigation and the salts contained in the water start being taken up by the roots.  These “extra” salts need to be leached; otherwise, they actually compete with the tree for soil water.  By “extra”, these are the salts like sodium and chloride that can be harmful to the tree, rather than the nutrient salts that are necessary for tree growth, but will also be leached when trying to achieve a balance by removing the harmful salts.

So there are several steps to follow to figure out a droughted tree from a root rotted tree.  If the tree is stressed from drought, eventually though, it quite likely can lead to root rot.   Looking at wilted leaves is an indication of a stressed root system which is common with a lack of water, but can happen when the roots are soaked for too long from rain, a leaky irrigation system or sediment accumulation that can occur with flooding.  Wilting is also one of the first symptoms of root rot, because there are not sufficient roots to keep up with the tree's water demand.

Step I. Wilting

Wilting is going to be the first step in alerting you to a soil/root/water problem, but it is just the first alert and there are more steps to a field diagnosis.  The steps take on three different parts of the tree:

First, look at the canopy overall and then more closely in the canopy

Then, look AT the ground

Then, look IN the ground

If you look at the tree from a distance and the canopy is thinning with dieback (staghorning)

Step 2: Thinning canopy.

This means that it is something that has been going on for a longer time that just to cause the leaves to flag (wilt)

And when you look more closely, the leaves are small, yellow, have tip burn and there are lots of flowers

Steps 3, 4, 5: Small, yellow leaves; tip burn; profuse flowering

This again means that it's something that just didn't happen with a missed irrigation or two, or a stopped up emitter.  Something has been going on for maybe more than a season.

And if there is fruit, if it is sunburned which means it probably isn't saleable, it means there isn't enough canopy to protect income

Step 6: Small, sunburned fruit

Now you definitely know there is a problem with the roots. The roots mirror the canopy.  When they go wrong, they canopy goes wrong.  All these thinning symptoms in the canopy, also means the root system is thinning.  Also, when the canopy goes wrong, the roots have problems.  When the canopy can't feed the root system it is less able to fend off disease, if that is the cause of the thinning canopy problem.  At this point, it's not definitive that it is root rot causing the problem, but a sad canopy can lead eventually to a root rot problem because of lack of energy generated in the canopy.

The next step is to look AT the ground surface and see if there's natural leaf mulch.  If the tree lacks energy to produce leaves, there won't be any leaf drop and now leaf accumulation. These should be leaves in various stages of brown, indicating they have been there for a while.  This mulch protects the roots from drying out and also produces an environment hostile to the root rot organism. No leaves to feed the fungi and bacteria that compete and destroy Phytophthora, eventually Phytophthora will come to dominate the system. No energy to produce leaves; no canopy to protect leaf mulch from wind?  And, then the wind blows the leaves away.  On hillsides, gravity can act against mulch creation and also exposes trees to more wind, but a healthy tree can create its own mulch in harsh hillside environments.

Step 7: No natural leaf mulch

With a sick canopy and no natural leaf mulch, this is the time to think there is something seriously wrong.  There is something wrong with the water uptake in this tree.  Either a lack of water or a lack of roots.  Is it the timing, amount or distribution of the water? These are all issues that can be corrected if there is sufficient water to do so.  Maybe the soil is too wet?  It could be asphyxiation.  Lack of air.  That can be corrected by identifying the cause of the lack of air or too much water.

Step 8: Asphyxiation

But if the soil is not too wet, when you apply water, does the tree perk up?  Give it a couple of days.  This could always have been the problem.  Does the water come on?  Is a valve shut down?  Is the system not working?  Is there poor water distribution.  This infrastructure problem is common in hillsides irrigation with cheap parts that are easily damaged by coyotes, rabbits, and pickers.

Step 9: Turn on the water

But if the tree does not or has not responded to applied water, then start digging. It's time to look IN the ground. This is something that should be done on a regular basis just to see how those roots are doing, anyway. 

And when you start digging, there's no roots

Step 10: NO roots

Or only big roots

Step 11: Only big roots

And, if you do find any little roots, they are blackened and brittle

Step 12: dead root tips

And you have applied water and the tree doesn't perk up, then the tree probably has Avocado Root Rot disease caused by Phytophthora cinnamomi.

There can be other reasons, for a tree collapse like this, like a gas pipe leak, gopher activity in young trees, a chemical/fertilizer spill.  Probably other things that kill roots, but a field diagnosis like this process can pretty much identify the problem as root rot.  It can then be verified by a lab test to make sure.  However, there are times of the year and disease conditions when a test will come back negative and it might be necessary to retest with another sample at another time of year.  

Most groves that have been in the ground for many years and have been harvested by outside commercial crews quite likely have the root rot organism present in the orchard.  The lack of disease is because the stress that brings on disease is lacking – water management, frost/heat damage, flooding, too much rain, too much fruit, pruning, etc. – anything that predisposes the tree to infection.  It is when several stresses are present that the trees start declining and if identified soon enough can be corrected and the decline stopped and reversed.  

Posted on Monday, May 27, 2019 at 11:22 AM
Tags: avocado (287), cinnamomi (4), Phytophthora (23), root rot (21)

Mature Compost Does NOT Kill Phytophthora

A recent article in California Agriculture highlights something that we have found in raw organic materials that have been used in mulches for controlling Avocado Root Rot – Phytophthora cinnamomi.  The most active stage of a material in the process of composting, is the initial one where all the bacteria and fungi are fighting to consume the easily decomposable sugars and light fraction organics.  That's when the material heats up and various gases, such as ethylene, ammonia and others are released.  This is the most competitive time in decomposition and Phytophthora just can't compete.  In fact, it becomes a food source for the antagonistic fungi, since its cell wall is made of cellulose the material that many leaves are made of.  In releasing exudates to decompose cellulose, the Phytophthora is decomposed, as well.  As the cellulose is decomposed and disappears more resistant materials remain.  A mature compost, is therefore a much more stable material than a raw one.  It still has nutritional benefits, as well as physical effects on soil when it is incorporated, but has a lesser impact on Phytophthora. 

Compost is used as a soil amendment, largely because it is relatively stable biologically and has nutritional/physical effects. Incorporating raw organic matter into the soil and then planting has its restrictions and should be done cautiously.   But as a mulch (material applied to the soil surface) there are fewer problems, as long as some common sense is used.  Like don't pile it up against plant stems which keeps moisture and conditions for disease around the plant crown.  And there are several other qualifiers, such as don't apply it so thickly that the soil never dries out and becomes a problem in walking across it. 

So, read this interesting story of what happens to Phytophthora when introduced into a mature compost:

This is also a great web site to read about other UC related agriculture and natural resource research.  Sign up.

compost pile
compost pile

Posted on Monday, January 18, 2016 at 7:02 AM
Tags: cellulose (1), cinnamomi (4), compost (7), mulch (13), Phytophthora (23), ramorum (1)

Avocado Dieback – Blight vs. Phytophthora vs. Lack of Light

When you see dieback in an avocado it could be due to several reasons, and here are three very common causes of dieback, one of which has been especially common when there is little rain. The first major cause of dieback is an overgrown tree where there is no light that penetrates into the canopy. Branches with leaves in a darkened interior will naturally shut down and dieback, leaving these twiggy dried out branches. This is a natural process whereby the tree just gets rid of leaves that are not performing.

Another cause of dieback is our old friend Avocado Root Rot, Phytophthora cinnamomi. This causes dieback, also called “stag horning” because of the dead branches standing out from the surrounding canopy. This is normally accompanied by a thinning canopy with smaller, yellow leaves and a lack of leaf litter because of lack of energy. It's also hard to find roots and if they are found, they are black at the tips and brittle.


The third major cause of dieback is a result of water stress. This shows up with low water pressure, at the top of the hill where the most wind occurs, where a sprinkler gets clogged, when the irrigation schedule is not meeting tree's needs or when there is not adequate rainfall to get sufficient leaching. And after four years of drought, this is very common. This appears as dead spots in the canopy, a branch here and there where the leaves have died and are still hanging. It's been called “salt and pepper” syndrome, because it can have a few branches here and there that have died back while the rest of the canopy is normal, the leaves are normally sized and green. In young trees, in severe cases, the fungus that causes this blight can work its way down to the graft union and kill the tree. In mature trees, it just causes an unthrifty look to the tree. Although we have always seen this problem in avocado orchards, this has become a very common affliction in orchards these last few years


1)      Lack of light dieback

2)      Phytophthora cinnamomi dieback

3)      Stem and Leaf Blight

lack of sun
lack of sun

root rot vs healthy
root rot vs healthy

stem blight
stem blight

Posted on Wednesday, May 13, 2015 at 9:28 AM
Tags: avocado (287), Botryosphaeria (12), cinnamomi (4), dieback (4), Dothiorella (13), leaf blight (8), light (2), phytophthora (23), stem blight (2)

Signs of Avocado Root Rot

In the last two weeks I’ve been out to see groves that have root rot, yet the growers did not recognize the signs.  Two years of drought and use of salt loaded water have put stress on trees and made them more susceptible to root rot.  Although irrigation management can bring about the symptoms of root rot – small, yellow, tip-burned leaves – because the tree in both cases is seeing a lack of water.  I thought it would be appropriate to review the symptoms of avocado root rot.

What to look for:

Small, yellow, tip-burned leaves

Thin canopy

Die-back in the canopy, causing stag-horning (dead stems)

Little or no new leaf growth, hardened look to the leaves

Few or no leaves on the ground (tree doesn’t have energy to produce leaves)

Profuse flowering and small fruit

Sunburned fruit from reduced canopy

Then get on your knees and dig around in the wetted area of the root zone

Do you find roots in the top 3 inches of soil?  NO, that’s a bad sign

Do you find any white root tips (it’s hard to find these when the soil is cold in the winter)? NO, that’s a  bad sign.

Do you find black roots?  Yes, that’s a bad sign.

These are all field diagnostics for avocado root rot.  You can also sample roots and send them in for lab analysis, but in the winter, the root rot organisms are not active and you can actually get a false negative.  Meaning the lab won’t pick it up and you then think you don’t have the disease.  Use field clues to figure out whether you have root rot.  Then figure out why you have it.  It usually boils down to the amount and timing of water, but there are many other factors, such as water quality, fruit load, topworking and other stresses that can bring on the disease.

Images.  Root rot in canopy, leaves and roots

root rot canopy
root rot canopy

root rot leaves
root rot leaves

root rot roots
root rot roots

Posted on Monday, October 21, 2013 at 7:39 AM
Tags: avocado (287), canopy (5), cinnamomi (4), leaves (3), Phytophthora (23), root (1), root rot (21)
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