Plant Pathology

Key terms and concepts in order of appearance

abiotic vs biotic disorders; vector carriers; the plant disease triangle;
monocultures; pathogens and infection; mycorrhizal, parasitic, saprophytic lifestyles; antibiotics; Integrated Pest Management; mechanical, chemical, biological and cultural control; disease resistant varieties; overhead water; plant pathogen specificity; bacterial pathogens; viruses; variegation.

Plant pathology

Plant pathology is primarily concerned with fungus, bacteria, and viruses. We will talk about their life style and life cycle in a bit. First some prehistory.

Plants like all creatures get sick and die. We have observed this since ancient times. Spots and blotches and the smell of rot. Wilted seedlings, distorted and twisted foliage. Scabbed and mildewed fruits. In the old times, before microscopes, we were not able to identify the microorganism that caused the disease. But, we could certainly see their symptoms and effects. And we learned that wet weather at harvest time, followed by some warm nights, was sure to end up spoiling the crops. On a large scale, a disease outbreak is called an epidemic. And if people were dependent on this one food crop, and the crop failed, famine was not far behind. Then its fighting, migration, and aberrant behaviors like cannibalism and genocide.

Plants have been fending off attack from pathogenic organisms for hundreds of thousands of years. This is why there are protective things like bark, pine pitch, oils in the lavender and rosemary, and latex canals in the stems. In other cases, plants would form beneficial alliances with certain fungi, which would allow them to fend off attack from other harmful and virulent fungi. Plants in a given population would be diverse in their genome, and hence harbor resistance against malevolent forces. So if one went down for this or that, the others might survive and pass on their beneficial traits. Nature’s workings – kinda like putting your eggs in a bunch of baskets to ensure survival, just in case.

Plants live within a comfort range that is based on their place of origin and evolution. Some like clay, others like sand. Some don’t mind sitting in water all day long, others want it always well drained. Some like it hot and tropical, others like it cool. These environmental factors we call abiotic. A – biotic = not of a living thing origin. These are things like temperature, humidity, water and light needs, and soil nutrients. If a plant is not living within its happy range, it gets stressed out. It can die, or become more susceptible to attack by creatures that ‘sense it is weak’. There are hordes of hungry creatures constantly on the prowl for food. It is like the motif of the snake eating its own tail. Nature is not all harmony and peace, it is a constant feeding frenzy.

An interesting relationship between plants and people grew out of the process of domestication and agriculture. In the wild, plants are tough, independent, loaded with spines and poisons and alkaloids, and relatively restricted to a certain area. But with humans cultivating them, they gave up a lot of their own defenses, and went cosmopolitan. They became softer, tastier, and unable to cope on their own. Rather than being individuals living in a jungle or a meadow or on a mountain top, they became a huge monoculture of clones living in rows with nothing else in between. And so this made them extra susceptible to ever present pathogens that were specific in their targets and always looking out for ‘easy game’ and ‘low hanging fruit’.

The pathogens are tiny and move easily. Anything that moves the pathogen from here to there is called a vector. Vectors can be abiotic – like the wind or water. Or they can be biotic – of a living thing – like animals or people. Pathogens can enter through the breathing pores of a plant, through the irrigation water and the roots, or through a cut, an opening, on the plant’s body. The most common biotic vector in town is a probably a gardener armed with a pair of pruners going from neighborhood to neighborhood. Or a gardener spreading pathogenic soil amendments. Or rodents chewing and tunneling and running hither and tither. Vectors that move disease worldwide are things like the ballast water of ships that is sucked in and pumped out of the sea at various ports; the wood pallet beneath the imported furniture with hitchhiking insects; and the spores carried in the muddy grooves of a pair of hiking boots.

Once the pathogen gets inside the plant, then it is infection and invasion. Take over, feed, move on. The disease wants to keep spreading and disseminating some more. It may form reproductive type structures that further its colonization, and disperse when the timing is favorable. The disease cycle can be stopped or wind down a bit if there is a freeze, a fire, or if the pathogen itself comes under attack by another pathogen. It does its thing, and fades into the background. The diseases are always around, but just do not exhibit themselves and take control unless the environment is suitable, and the hosts are weak and susceptible. This is known as the plant disease triangle of a successful infection.

In order to understand plant pathology we will describe a few local examples, and their solution or cures, if any. We will start with fungi. For some reason, as important as fungi are, people don’t pay much attention to them. Aside from the mycophiles who adore truffles and winter forays for chanterelles in the woods, most people are pretty much blind or ignorant of fungi. Or look upon them with great disgust and fear. They are a major and ancient group of organisms that date back probably a billion years. They, along with plants, make life possible on our planet.

Then you ask people – “Do you drink beer? Do you eat leavened bread? Bread that is puffy?” And they are like, “Sure!”. Well the yeast that makes that all happen is – a fun gi. And that alcohol? Thats its waste product. People like “What?! I’m drinking what?!”

Fungi are the primary cause of plant disease, in the ballpark at 80% of all plant diseases. On a more positive note, they also form a symbiotic relationship with plant roots and they help each other survive. These fungi are known as mycorrhizal fungi, and this mutualistic enterprise is said to occur in around 90-95% of all land plants. So it is not all bad, the scale tips towards working together.

Plus, along with soil bacteria, fungi are our primary source of life saving antibiotics. Think about that word – anti biotic. A substance that kills or is against living stuff. Chemical weaponry that fighting creatures use on one another, now re appropriated for use by us. Pretty cool stuff.

One fungus that eats trees around here is the oak root fungus. It infects trees through the roots. Its body of fine white strands of threads of cells takes over the vascular system of the tree and feeds and feeds. Eventually it clogs the tree all dead. So in the beginning it is like a thief – a parasite, it takes takes and takes while the host is alive. Then when the host dies, the fungus starts to eat its dead body too. It becomes a saprophyte, eating dead stuff to live. Two distinct life styles. Not all the fungi are this versatile, some are restricted to one or the other…

In the winter time, the oak root fungus sends up fruits to disseminate its seeds, so to speak. Except in fungi the fruit is called a mushroom, and the seeds are not seeds, they are spores. The easiest way to see spores is to take that portobello or white mushroom from the store and lay it gills side down on a piece of white paper overnight. Then you can see it drop all its spores. What color are the spores? (LAB)

The oak root fungus mushrooms are densely colonial and emerge in great numbers all together in the wet humid months. They drop their white spores that float out on the wind, hopefully to find another plant victim and continue the cycle.

So then if you are a gardener, a tree lover, what do you do? What are your options for dealing with such an “enemy”? Here are some of the scenarios:

If the soil dried up, the pathogen would not be able to spread so easily. If we did not irrigate the lawns and soils of Golden Gate Park, the pathogen would not be so abundant. But we are not turning back the clock and letting the sand dunes take over again. The water regime is here to stay, more or less. Nor is it feasible to remove all the soil and truck in brand new soil. Good luck, no go. So we are sorta stuck, abiotic factors wise.

If we removed the mushrooms every time they popped up, that might cut down the spread of the infection. A teeny wittle bit. But the actual organism is underground in the soil and in all the buried wood and roots. So even if you could get every mushroom before it opened to release its spores, taking away the mushroom does little to the actual organism.

Couldn’t we just kill them all and poison the fungus? No is the answer. It would be hard to treat and spray the soil to that extent. Unless you want to live in a hell of poison and gaseous death. People would be keeling over long before the fungus raised the white flag. Plus the fungus would likely come right back without repeated over and over again spray regime. Even then…

If we ate the oak root fungus, that could keep its population down. We would have to promote it as the most fashionable and cool thing to do. They are edible and pretty tasty. Plus there are a lot of them. As for whether they have accumulated heavy metals or other toxins present in the urban environment – not sure, pass. Probably best to be moderate or conservative if you plan on eating them regularly. Likely not the best of plans…

Okay to tally thus far. And inoculate you with this broad concept of dealing with pests called Integrated Pest Management. We do not control the abiotic factor known as the weather. We cannot stop the wind, eradicate the tides, or fight the climate. If you war against the earth’s forces you are sure to lose. We can adapt to changes, and help make the planet a livable happy place, but the mentality that somehow you are going to ‘win’ does not cut it. Life is life, not a game. It is not the appropriate metaphor for the pickle that we finds ourselves in.

In Integrated Pest Management, there are four basic methods for controlling pests. These are ways to keep pests at a tolerable threshold so that life can go on and we are not starving and dying, nor having cockroaches for overlords. When you remove the mushrooms by hand or with a tool, that is classified as mechanical control. When you spray stuff on em to kill them, that is chemical control. And when you or another animals eats the pest, that is biological control. With fungus, given its tenacity and power, our best general strategy is cultural control. These comprise preventive measures that minimize the growth and spread of these creatures.

There are many plants naturally resistant to oak root fungus. So ideally, we would only plant these plants. This is one method for how we manage many or most of our orchards of citrus and nuts, and our plantations of banana, potato, and so on. Plant the variety that is not going to get sick, the ones that are immune and are not so susceptible to the particular disease pathogen.

Another fungal disease that is common in our garden worth discussing is one called powdery mildew. It looks like well, a bunch of white powder on the surface of the leaves. Unlike the oak root fungus, this fungus does not make a mushroom. It does, however, make a little sac of spores for dispersal purposes.

In the garden, powdery mildew spores are floating around in the air, coming in with the summer fog, and if they should land on a tasty wet zucchini leaf on a nice warm day… They will germinate and grow, and then it is feeding time!

So lets run through our options. Protest the fog and activate the movement to ban low clouds full of moisture. Uh no. Invent a massive filter and fan to clean all the outdoor air of every single pathogen spore. Also no. Try to stick to things that are actually feasible and practical. Scrape every leaf clean by hand? No. How about a spray of some kind? Well you can kill the spores before they germinate, but once the fungus is in and feeding, it is hard to eliminate with the chemicals. Chemicals are best used as a preventive, not as a cure. Biological control wise, there are bugs that do like to eat powdery mildew, but it would be a stretch to have enough of them around to make a dent. So where are we? Back to the cultural preventive controls. If your leaves are not wet, then spores have less of a chance of germinating. If you keep the area clean of old dead leaves full of spores, less likelihood of infections. So keep overhead watering to a minimum, keep leaves dry, clean up the dead stuff full of spores, and plant your zucs with airy open spacing in a sunny spot. Thats about the best we can do.

Fungus is down. Next up is bacteria. Tag team duo.
One of the bacterial diseases that strikes plants around here is called fireblight. When a plant gets infected its branches look all burned and turn black. The vector or carrier can be insects flying from tree to tree, the rain splashing bacteria, or a gardener making open wounds with a dirty saw.

Many pathogens are specific in who they attack and feed on. This is called plant pathogen specificity. Fireblight is partial to members of the rose family. The rose family (Rosaceae is the proper name for the family) has many many members, not just the roses. Fruit and nut tree wise – almonds plums cherry peaches apples pears nectarines loquats quince medlar are all in this family. Berry wise – blackberry raspberry strawberry. Ornamental wise there is Spiraea Potentilla Geum firethorn and hawthorn. Weed wise there is Cotoneaster. The most common ones we see with infections around town are the street trees like ornamental pear or flowering plum. One day it looks healthy and happy. The next day a shoot or a branch is all inflamed and darkened. Sometimes a sore of a canker forms. And more die back down the line. Followed by more goopy ooze and more bacteria…

Bacteria are funny creatures of an ancient lineage. They are everywhere. Again, they get a bad rap with the antibacterial soaps and anti bacteria wipes and solutions that kill 99.9% of all bacteria. Truth is most of them are helpful and beneficial and we would be dead without them. Whether as members of our own intestinal fauna, or as members in the soil responsible for recycling and nutrient cycles and exchanges, bacteria have important jobs and deserve our recognition and respect.

That said, I did not like the staphylococcus bacteria that gave me swollen bloated limbs and brought me to the brink of sepsis then amputation twice. Nor do I enjoy seeing my bag of potatoes in the cabinet succumb to bacterial soft rot and ooze all over the place with that stinky nasty smell. Still, I do not intend to go to war against all bacteria. That would for sure be a losing battle.

In the yard, if fireblight is present on a rosaceous plant, we cut off the infected limbs and try to contain the infection. If you cover the wound with a clay slip, that may be helpful. Maybe. And we disinfect our tools in between uses with lysol spray, or a little propane torch, or alcohol. That is about all we do. Bacteria like warm and humid conditions, and feed and multiply once they somehow get a foothold into their prey and host.

In humans, when we have bacterial infections, we use antibiotics like penicillium or amoxycillin or clindamycin, depending on the type of bacteria and the location of the infection. The source of all of our antibiotics are fungi and soil bacteria. These medicines are liquid substances that fungus and bacteria use to repel one another in their competition for food – bits of decayed leaves or the skin of a gopher. In the recent past, before the invention of antibiotics, peoples would use natural substances of a similar effect to treat wounds. These included things like honey, plant oils and resins, clays.

There are some rare instances where we will inject tree trunks with antibiotics also. But this is usually not done because it is expensive and does not always work. So we live with our companion and occasional foe with awareness and caution. Bacteria.

Last one – viruses. Then we all go home to rest
okay ‘higher’ fungi grows as little threads from a spore
finds a compatible mate amongst four distinct sexes
forms a massive pulsating underground network called mycelium
and congeals together into a shroom to spread more spores

bacteria divides itself over and over again
and it become stronger, more diverse, and more resistant
by exchanging bits of genetic material with each other
so no sex, just a little hand-off time to time
they come in all shapes and sizes
and move around together beating their little tails


Size: super little

Lifestyle: get in, get em to make more of me, everybody out.

Structure: a secret instruction code surrounded by a protein armor that functions as a spy, camouflage, and attack organ.

Effect on the plant: If the plant is working on making virus bits rather taking care of its basic duties, then the machinery is gonna get gunked up and malfunction. Viral infection results in leaf splotting mosaic patterns that are not green in color, rings of dead tissues on the stems, stunted plants that look like a permanent wax museum bonsai, and leaves curling and twisted with tiny gouged holes like it had been hit with tiny size #20 shot if there was such a thing.

Vectors and manner of dispersal: insects with a mouth and a gut full of the virus, feeding and spreading, feeding and spreading. A gardener grafting a scion piece to a rootstock piece, inadvertently serving as an in between. A farmer touching and cutting plants while walking through the crops. A tiny round worm in the soil sucking here, then sucking there. Virus hiding out in the seeds, and going where the seeds go.

Specificity: Not sure. For the most part as far as we sorta know, plant viruses stick with plants, and do not infect animals and humans. More work needs to be done to elucidate results…

Application: biotech companies using plant viruses as messengers and bosses to inject into plants and have them perform specific functions. Purposely encouraging plant viruses that create cool looks like ‘red tulip flower streaked with white’, “lime orange New Zealand flax foliage”, “spotted snake plant” and “polka dot yellow griselinia”. Sometimes this is called variegation.