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It's alive! soil macro and micro organisms

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Cjay R

on 12 June 2014

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Transcript of It's alive! soil macro and micro organisms

It's alive! Soil macro and micro organisms
Supporting good critters, the soils immune system
Soil Macro-

Soil Micro-Organisms

Macro means large enough that you can see it.

and bugs

There are a lot of living things in soil!
Worms, bugs, mites
can be helpful or harmful to plants.
Most are good for soil
because they break down organic matter and waste, their excrement can be a source of nutrition for micro organisms, and it helps bind the soil together and hold nutrients in.

Macro organisms also loosen the soil and help create pores for air and water.

Of course,
some cause problems
and need to be controlled.
Ants- friend or foe?
Many species of ants are considered beneficial. They loosen and turn a lot of soil - as much as earthworms do, and create pores for air and water from building their colonies.

They help break down dead organisms so bacteria and fungi can finish decomposing them.

Ants are also predators and kill and eat many species of harmful insects.
Ecosystem Engineers
There are a lot more creatures that live in the soil- like these- that we won't talk about today.
There are a lot of "big" creatures that live in the soil, today we'll talk about these:
Worms mix and move soil around. Charles Darwin called them "nature's plows" because of how they mix topsoil and lower layers of soil.

Worm "castings" are excellent fertilizer.
As worms tunnel through the ground, they make space for air and water to reach plant roots.

Pores and tunnels created by worms help soil absorb water, reducing runoff and puddling.

Reducing runoff maximizes the effectiveness of fertilizers, and prevents pollution.
Worm poop also directly feeds plants. Investigations show that fresh earthworm casts are several times richer in available nitrogen, available phosphates and available potash than the surrounding topsoil. Worm castings also contain many beneficial bacteria and protozoans.
Want worms?
There are different species of worms that are better for eating compost or foraging on their own.

You can keep worms in a bin- and feed them compost frequently.

Worm castings include undigested organic matter, which becomes smaller and has more surface area- perfect for bacteria and protozoa to finish decomposing.
Ants gone bad
Ants can do too much borrowing and loosening of soil, and can disturb crops.

Black ants are considered among the helpful species.

But here in Hawaii we are seeing infestations of fire ants- those are not our friends!
Ant Control
Unfortunately, there are very few natural ways to control ants. Prevention is the first step- fireant infestations can come from soil and green waste, or compost that wasn't heated hot enough.
There are ant baits and poisons that can be used to kill ants. Pesticides are the only known option for controlling colonies at this time. In an infested area, neighbors will have to treat their land at the same time to prevent re-infestation from an untreated area.
Our new worst enemy
Fireants are so invasive they are causing damage to crops at nurseries and farms. It is estimated they could cause more than a million dollars of damage a year.
Fireant stings cause painful and itchy welts.
Good and bad aside, ants are pretty cool. This is a plaster cast of an ant colony- that dug over 8 feet into the ground!
Beetles and bugs that live in the soil can eat crops or eat pests- it all depends on the species.
Pillbugs feed on decaying matter- they're a good sign in a compost pile
But if your vegetables are touching the ground, they might eat them.
Pillbugs are a good example of how bugs can be "good" or "bad"
Beetles may
eat leaves of plants. Squash borers infect the hollow cores of squash stems, slowly killing the plant.
Control of beetles, bugs and other insects can be done with a variety of methods.
Baits and traps can be set for some bugs, luring them to their death with pheremones
Poisons and sprays can be effective for certain types of beetles and bugs, on certain crops. Bugs with hard bodies may be more resistant to pesticides than those with soft bodies.
It's really important to know what insect you are trying to kill so you can target it- not all pesticides work on all bugs. You might waste money and harm your garden or farm's ecosystem and not even stop the damage to your crops.

Sometimes a plant disease or bacterial infection will look similar to damage from an insect.
The beetles you do want
Here a ladybeetle larvea feasts on a red aphid
Many beetles and bugs spend part of their life cycle underground as larvae, and emerge as adults.
The beetles you don't want.
Some beetles, bugs and insects are predatory of the bad bugs, and will eat larvae, nymph and even adult bugs that harm your crops.
You can attract the good bugs by growing the plants they like, or purchasing them to release on your land.
Most of the bugs and beetles you'll see are harmless.
If you do have an
Most mites are microscopic
There are some that are just large enough to see.
A lot of mites are harmless, and are food sources for other predatory creatures that live in the soil.
Some mites feed on plants, drinking their sap, eating their leaves, and causing growths and diseases.
Eriophyd mites caused this leaf damage
Mites can be controlled with chemicals sprays or natural substances like sulfur.
Having a healthy balance of air and water in the soil, as well as "good" bugs is the best way to control mites.

Mites often do damage when ecosystems are already out of balance, such as a during a drought or a flood.
As worms eat their way through the soil they leave behind valuable nutrients for bacteria and plants.
Some live primarily in the soil for their whole life cycle. Others stay above ground once they have grown out of the larval stage.
One teaspoon of soil can contain as many as 5 billion living organisms. That's more than half as many people are on the earth!
What are these creatures?
(tiny bugs)
Arthropods have jointed legs.
On the macro- scale they are "bugs" beetles or mites
On the micro- scale they can't be seen without a microscope.
, arthropod's primary job is to shred and break down organic matter so it is more available to bacteria and fungi. Their mouthparts are hard enough to break down things like wood.

Arthropods also eat bacteria and fungi, keeping the populations in check.

They loosen and aerate the soil, and their waste matter can feed plants.
As with any part of an ecosystem, if it's not kept in check by other creatures, arthropods will take over and start decomposing living plants.

All ecosystems have food webs where predators, prey, and plants live in balance because they control each other's growth and expansion.
Mite damage can be difficult to diagnose
You might find visible networks of mycelium if you dig around compost piles or old trees.

(tiny worms)
Protozoa feed on smaller bacteria. This keeps bacterial colonies in check. Because of their size, protozoa are an important part of the food chain- they are eaten by nematodes and arthropods.
In the picture below you can see a protozoa eating a long, threadlike bacteria.

Protozoa are a lot like bacteria- single celled organisms that can be harmful or helpful.
You may never hear about protozoa again, but they are part of the vast ecosystem present in healthy soil.
Protozoa size can range from a few microns (micrometers) all the way up to a millimeter. Most bacteria are only one micron in size
Nematodes are microscopic worms, or parasites. Here they have just killed the larvae of an invasive bug.
Nematodes are tiny roundworms. They are well known enemies of the farmer and gardener. They can devastate pants and be difficult to kill. Sometimes an entire crop could be lost to nematode destruction. Worldwide, up to 15% of crops are lost due to nematodes.

Nematodes are also well known as heroes, some species being the most effective biological insecticides available. Beneficial nematodes sprayed on infected crops can kill pests within a couple of days. This would normally take weeks to treat with chemicals- the beneficial ones do this all with no damage to the environment or human health.
Nematode damage
These carrots were infected with a nematode that moved in to permanently feed off of them. There is no treatment for the carrots, only for the soil, and these can't be saved.
These are all pictures of nematode damage
Damage to a field of soybeans
The harmful nematodes have piercing mouthparts, that inject enzymes into a plant cell and suck the juices out. They usually attack plants from the root, sometimes they attack stems leaves or fruit.
Beneficial nematodes attack insects that destroy plants.
Beneficial nematodes infect hosts with bacteria that eventually kill them. Above- A nematode's head and mouth, covered in bacteria.
Nematodes infect a host, and lay eggs, which gestate inside the host body and emerge when grown. Here, freshly hatched nematodes leave a dead beetle larvae.
Plants respond to nematode attacks with swellings, dead areas, and distorted growth.

Nematodes can also infect plants with viruses and fungi they carry.

Sometimes it's obvious, and sometimes it is hard to determine when nematodes are the cause of damage to a plant because the symptoms are similar to other problems such as viruses, nutrient deficiencies or pollution.

To be sure, a soil test is the best way to determine if damage is from nematodes or lack of nutrition.
There are 20,000 to 80,000 species of nematodes that have been identified, good, bad and neutral.

You can purchase some of the "good" ones specifically to target pest problems.

By infecting the pest or it's larvae, beneficial nematodes can eradicate some pests within a day or two. This is one of the most effective biological pest control methods available.

Using biological pest control methods such as nematodes is increasingly popular because it is cheap, effective, and causes no damage to the environment.

They can be called "bio-insecticides."

It's important to know what pest you are targeting to get the right nematode to eradicate it.
Nematodes don't just infect plants. Some of the bad guys infect livestock, and even people. Infections can come from ingesting undercooked meat that was not processed well, or from food contaminated with feces. One reason proper food safety practices are so important when harvesting.

If infected, animals and people have to be "de-wormed," taking herbs or pharmaceuticals to kill the bugs. Some livestock routinely get chemical "drenches" to remove any worms living on their fur.
The bad:
The good:
Nematodes are everywhere, and fortunately most of them are actually beneficial to your farm or garden.
Using nematodes as a biological pest control is effective for many pests and poses no danger to people or the environment.
Nematodes cause billions of dollars of crop damage each year around the world.

Once a crop is infected, many times there is no solution but to plow the crop under and use physical, biological, or chemical control methods to prevent the next crop from being destroyed.
What can be done?
The stronger the "Immune system" of your soil is- that is- with a healthy community of macro and micro-organisms, and a good balance of air, water, and available organic matter in the soil- you are likely to have fewer nematode problems, and more of the good ones.
If a nematode infestation occurs, there are chemical, biological and physical treatments that can be used to control the infestation.
A predatory nematode eats another nematode.
The Ugly
Most bacteria in soil are so tiny they are only one micrometer long- you could fit 1000 of them in a millimeter.
This is the tip of a pin, covered in bacteria!
Many soil bacteria are
, finishing the process of breaking down dead plants or fecal matter into molecules that are small enough to be absorbed by plant roots.

These nutrients could be eroded and washed away, but bacteria help soil retain nutrients over time. When bacteria die they
slowly release the elements they've stored in their bodies
, helping soil stay fertile longer.
90% of all living organisms in soil are bacteria.
piercing mouthpart ----->

Worms literally eat their way through soil, chowing down on organic matter as well as loosening clumps of dirt.

Looser, aerated soil makes it easier for plant roots to grow down deep.

Some worms borrow vertically, some horizontally
On a farm, some pesticides, or the use of too many inorganic fertilizers can make the soil too toxic or acidic for worms to live.
Some pesticides are safe for worms, others, such as Sevin, kill worms immediately.
Fire ants eat seeds, and destroy plants.

Rather than help control pests like some ants do, fire ants by "farming" problem bugs like aphids, white flies and scale insects, promoting their growth.
Plant and bacteria relationships are usually symbiotic.
Plants make their own food by the process of photosynthesis. They exude some of that food (10%) through their roots to feed bacteria and fungi- who in turn provide nutrients for them.

The area around the roots where plants exude (release) food is called the rhizosphere.
The Rhizosphere extends 5mm out from the plant root. This is where most of the microbial and fungal action happens- right next to the root.
In the rhizosphere, or root zone, soil has different biotia and different properties than soil where nothing is growing.
Nitrogen gas is abundant in the atmosphere- the air you breathe is almost 80% Nitrogen. So why do plants need help to get enough?

Plants can't absorb nitrogen i it's elemental form (as a gas) they need to drink it in through their roots in a water-soluble form. Bacteria take atmospheric nitrogen (N2) and "fix" it to another element such as oxygen or hydrogen to make it absorbable. (NO3- or NH4+)
Some bacteria are free-living and fix nitrogen into the soil.

Others, called rhizobia, move into the roots of legume family plants and form nodules where they fix nitrogen directly into the plant. In exchange they are fed and have a safe place to live.
Rhizobia nodules on a pea plant.
Plants with and without beneficial bacteria.
For hundreds or maybe thousands of years, farmers have grown certain crops that increase nitrogen in the soil by partnering with these beneficial bacteria. (The rhizobia) When the plant dies or is plowed back into the ground and decomposes, the soil is made richer in nitrogen. The next plants to grow there benefit from the enriched soil.
One element plants need is Nitrogen (N). Plants use N for photosynthesis, and it's especially important during the time plants are growing stalks and leaves. The only problem is plants can't get it without help. Some bacteria "fix" nitrogen into the soil, or directly into plant roots.
Bacteria release sticky, slimy substances that bind the soil together, making it possible for other organisms to make pores and tunnels, allowing air and water in.
But wait, there's more!
Aeration and good water filtration are essential for plants and the community of micro organisms that live in soil.
Most good bacteria are aerobic, meaning they use oxygen. (The same way humans need to breathe oxygen whey they do "aerobic" exercise.)
Anaerobic bacteria don't use air- and are often not healthy for plants. In anerobic environments, such as a flooded area, the bacteria that thrive are not beneficial, and will cause more damage than good.
Whats the difference? between bacteria and protozoa?
Bacteria are prokaryotic cells- the oldest form of cellular life on the planet. Their cell structure is more simple. Eukaryotic cells like protozoa have organelles and their DNA is contained in a cell nucleus.

Protozoa are newer and more complicated cells than bacteria.
more complex cell - with organelles
simple cell no organelles or nucleus- (bacteria)
What you can remember about
is that they are
similar to bacteria
, they are
, they are rarely involved in plant disease or wellness, and they are an
important part of the soil food chain
Friends and enemies- it all depends on the species
tomato plants withering
the leaf of an infected plant
healthy onions vs nematode damaged onions
Why is it so great to have bacteria living in the root zone?
Bacteria change the chemical composition of molecules, in the soil making them available to plants in a form they can use.
Anaerobic bacteria are responsible for breaking ammonium, nitrites and nitrates back into atmospheric nitrogen (N2) in a process called denitrification.
Neither humans or plants can live without bacteria.
The same way bacteria provide nutrients for plant roots to absorb, good bacteria in the human digestive tract (probiotics) make it possible for people to digest food and absorb nutrition from what they eat. Bacteria live all over our bodies, in fact there are 10x more microbial cells in our bodies than human cells! (Luckily, they are much smaller than ours.)
Only a few are bad for us and make us sick- the rest, we literally can't live without. The healthier the friendly ones are, the easier it is to fight off the bad ones.
Bacteria in soil
-decompose organic matter
-fix nitrogen and make other nutrients available
-bind soil particles together
-can cause disease in some cases
-take Nitrogen from the air and fix it to H or O to make it available to plants as Nitrites or Ammonia.
-can directly protect against disease in some cases
Bacteria on the tip of a root hair
Without nitrogen fixing bacteria, farmers have no alternative but to use chemical fertilizers to give plants the nitrogen they need.
What are chemical fertilizers?
Usually made of ammonium nitrate, chemical fertilizers provide an abundant source of nitrogen in a form that plants can readily absorb. The plant makes no distinction where the nitrogen comes from, and is just as happy with nitrogen from any source.
Plants invite friendly bacteria to hang out by their roots.
Roots giving off nourishing liquid full of carbohydrates.
10% of a plant's energy goes to feed an under ground microbial community.
That's not all
If you weren't already a fan of bacteria- check this out!
A few strains of bacteria actively fight off pathogens that cause disease.
Not all bacteria are heroes, but some stop disease caused by fungus or other pathogens.
With the right bacteria, soil can fight off disease and keep plants healthy!
They're not all good...
Bacteria do cause disease in plants.
Symbiotic means mutually beneficial- everybody wins.
nice rizosphere!
There millions of strains of bacteria. Of those, there are about 200 strains of bacteria that are harmful to plants. They are more active in hot and humid climates.

Plants infected by pathogenic bacteria may droop or wilt, start oozing liquid, get holes or spots in their leaves or fruit, Or form "galls" lumps or tumors. They may turn yellow and die.
Bacterial infections are hard to treat. The plant needs to be removed and destroyed to prevent infections from spreading.
Bacteria have no mouths, so they have to digest food by excreting enzymes outside of their bodies, and then absorbing the nutrients through their "skin" or cell walls.

Most of the things they excrete, including their waste products, are good for the soil.
Why is bacteria goo good for the soil?
No mouth!

If overused, inorganic fertilizers can kill healthy soil life and can poison rivers and oceans.

The drawbacks are that chemical fertilizers are made in an energy-intensive process. Most are made from petroleum, which is increasingly expensive as oil costs rise.
Roots can only absorb what is near them, so a lot of N fertilizer applied to the soil is washed away- as opposed to N that is fixed by bacteria near or in the plant root.
Bacteria do an awesome job of breaking down waste, and making it into food for plants. By doing most of the work in the rhizosphere, they make nitrogen more directly available to plants, so there's less runoff.
When they eat, bacteria store some of the nutrients in their bodies. This gets released as they die and are decomposed by fungi or other bacteria- this acts like a time release mechanism, also making soil fertile longer, and preventing nutrients from washing away.
note how the damaged area is confined by the veins of the leaf.
Extra Credit
Soybeans- with and without rhizobia. The yellow leaves are a classic sign of Nitrogen deficiency.
There's not too much you need to know about springtails, other than they are very abundant in some places, and you might see them hopping around. Like most other bugs in the garden they are decomposers.
These lil guys aren't really mites, and they aren't beetles or insects, they are in a class of their own called "collembola."
Springtails get their name from an appendage they have (called a furicula) that acts like a spring, and allows them to jump 50-100 times their own body length.
They can jump so far because have a catch on their abdomen that holds the "furicula" in place, when they release it they fly up to 8 inches- 50 or 100 times their body length.
It's very rare these will cause damage to a garden. If they do it's usually by eating young plants or fruit.
Mushrooms are what people
usually think of
when they think
of a fungus.
The body of fungus is called mycelia.
Plant residues (both roots and shoots) are the source of food (sugars and carbs) for soil organisms.

There may be 1,000 times more soil microorganisms near plant roots than in soil further away from roots
Mycelia spread out far underground- meters or even miles, making a mat of interconnected fibers.
Fungi are such great decomposers, some species of them can be used to clean up toxic waste. Oil spills, industrial waste, pesticides, and biological toxins can all be cleaned up with the right fungi.
Remediation means repair of the environment.

means using mushrooms to repair the environment.
The mycelia that grow mushrooms are the kind that grow near roots but not into them. Here you can see the relationship these mushrooms have with the roots of a tree. (15% of mycelia)
90 to 95% of plants have symbiotic relationships with mycorrhizae. Mycelia are smaller, can reach out farther, and absorb nutrients better than roots can.
Almost all trees have relationships with specific mushrooms. Some couldn't live without them.
Whether or not you see them, you can be sure mycelia are everywhere. You can find them breaking down organic matter- around most living plants, and involved in the decay of many other things.

Fungi- the great decomposers
If you're looking for an amazing decomposer, capable of breaking apart hard, woody structures like cellulose or lignan, cleaning up toxic waste, or devouring oil spills- look no farther than our friends the fungi.
Bacteria are great decomposers but they aren't capable of breaking down as many things as mycelia can.
When plants have more access to nutrients, it helps them fight off pests and disease.
Among vegetables, only members of the
family- such as broccoli, cauliflower, kale, mustard, and
root vegeteables
like turnips, rutabegas and beets. - refuse help from mycelium.
Different strains
Hyphae, the individual strands of fungi that together, make up mycelium.
There are thousands of strains of fungi. Some are better at partnering with plants, and some are better at decomposing and cleaning up toxic waste products.
How about sarin and VX nerve gas? Yep, mushrooms can change them into non-toxic substances, too.
As with other micro-organisms - the specific issue you are looking to treat will require a specific strain.
So, is that
all fungi do?
Like bacteria, fungi make nutrients available to plants that they coudln't otherwise obtain.
Some fungi do produce mushrooms- but those are just the reproductive structures of the fungus that lives underground.

Fungi that work symbiotically with plants are called mycorrhizae
. myco= mushroom, rhizae= root. They make the rhizosphere (root zone) healthier.
hyphae- a thread of mycelium
These trees depend on mycorrhizae to grow.
Mycelia are Everywhere
That's not all there
is to fungi- in fact
most fungus stays
invisible,living under
the surface of the soil.
is made up of a dense network of thread like fibers called
(Fungi have a lot of names).
Mycelia can transport nutrients long distances, because the cells of hyphae are open to each other, allowing the flow of liquid and nutrients from cell to cell.
Scientists are finding out amazing things- like how fungi actually help plants communicate by carrying biological messages between roots.

The largest organism on earth is a fungus that spreads 2,400 acres- (1665 football fields) and lives in Oregon. It is estimated to be 2,200 years old!
What do they do?
are essential for the health of many plants. Not only do they increase the capacity of the plant to absorb nutrients, many protect plants from
. (
Pathogens are harmful creatures like bad bacteria
Some mycorhizae hang out in the soil near plant roots and make nutrients available in the soil. Others grow right into the root, then act like root extentions.

Relationships between mycorrhizae mycelia and plants are
Another word to describe the interaction that benefits both species is
Plant roots are larger, have thicker cell walls, and are many cells thick.
How do they do it?
Fungi can transform the chemistry of their environment very rapidly.
Most things on Earth are made out of the same elements- Carbon, Hydrogen, Nitrogen, Oxygen, etc. It's just the way they are arranged that makes them toxic or beneficial.

Many fungi can
re-arrange the
chemical structure
of toxic waste
products and turn
them into neutral
Here, oyster mushrooms clean up an oil spill
- the
, is an essential nutrient that's hard for plants to find. Luckily, mycelia release acids in to the soil that help make phosphorus (and other minerals) available.
Other minerals include potassium, copper, zinc, nitrogen and sulfur
Fungal diseases
Fungi are great at absorbing nutrients because their bodies are only one or two cell walls thick. They break down organic matter outside of their bodies by secreting
into the soil, and then absorbing nutrients through the cell walls of the
. (Similar to how bacteria digest their food, outside of their bodies.)
Plants love having
by their roots so much, they feed them the same way they feed bacteria- with root exudate.

Many plants feed 10% or more of their phytosynthetic energy as carbohydrates to bacteria and
. Some trees feed as much as 40%.
The best thing you can do for your body or your ecosystem is to create an army of good bacteria.
Fungi cause 75-80% of diseases in food crops.
Fungal disease killing turf.
Black Spot fungal disease infecting papaya.
Powdery Mildew
Bacteria and fungi are like minture chemical factories.
They can make complex molecular transformations in seconds. The only thing is they all need each other to survive and keep each other in check. Without a healthy ecosystem, any creature can get carried away and start causing problems.
Too many pesticides or fertilizers can destroy the friendly creatures plants rely on.
Even if you have a plant growing tall and without disease- it may not be able to absorb much nutrition if there's nothing in the rhizosphere.
Plants are happiest when there is a lot of life in the soil.
Pesticides and chemical fertilizers may do the job quickly. However over time, extended use will cause soils to have less fertility, and fewer nutrients available to plants.
By killing off the friendly micro-oganisms and bugs, the soil has no way to regenerate.
"Organic" isn't the only way, and sometimes pesticides and fertilizers may be necessary to save a crop, or to provide nitrogen or another crucial element to hungry plants.
Keep your plants and ecosystem happy by helping to maintain a balance of micro and macro-organisms in the soil.
The more you can create a happy environment for the good bugs and microorganisms, the less work you will have to do, and the happier your plants will be!
Micro means it's so small you need a microscope to see it.
The soil food web- Bigger creatures do the first steps in
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