Frogs have an anti-bacterial bio-film on their skin

Frogs have an anti-bacterial bio-film on their skin.  In fact there is an ancient Russian practice of placing a frog in milk to keep it fresh longer.    My bioponic systems are teaming with frogs and tadpoles.  Nitrification continues but it makes me wonder if I'm deriving a special advantage from the frogs that may help prevent diseases such as bacterial canker, soft rot, leaf spot, and wilt.  I rarely experience these problems, so maybe it's a gift from the frogs.  At night their singing it very loud but I like the sounds of nature..

Controling Nematodes

Rob Bob made a couple good videos about how he rid his wicking beds of nematodes.
For his ' Bugs, grubs & other garden critters.. ' Playlist click this link

Root knot nematode control using French marigolds & mustard 

Wicking bed prep for cool weather crops & root knot nematode update

Essentria_IC3

Essentria_IC3
http://www.envincio.com/essentria/product-dload/Essentria_IC3_PIB.pdf
This product uses an Octopamine Blocker which is a lot like adrenaline to an insect.  It over excites their nervous system and kills them.  I became interested in this product when I had a severe outbreak of ants in my aquaponic green house.  While it is safe for mammals and fish I would worry about using it around crustaceans.   It is broad spectrum so you must also be careful not to kill beneficial insects like ladybugs and bees.

I used this product in my house and green house.  I did find one dead cockroach in the garage where I dumped a very large amount of Essentria_IC3 mixed at the lowest recommended strength of 1/2 oz per gallon of water.   This same ratio did nothing to the ants and aphids I wanted to kill.

I then mixed 6 oz per gallon (the maximum recommended dosage) and sprayed heavily in the green house, and on a heavy infestation of aphids on my cabbage. Once again the product failed to kill anything including the aphids which received a heavy drenching.  I waited 5 days and then mixed the Essentria_IC3 at  96 oz per gallon.  Sixteen times the recommended strength.   The good news is it did not harm the fish and it did kill the ants.  The bad news is it destroyed many of my plants and the aphids have increased.  It may be a better herbicide than it is a pesticide.

I would not recommend Essentria_IC3.  It's was ineffective in my green house and garden.  The smell is horrid, and required that I air my house out for two days when mixed at the lowest ratio.

IMO Frass

Indigenous Microorganisms and Effective Microorganisms are used in Korean gardening methods where bacteria is fermented and grown, along with other beneficial organisms for the benefit of the garden's soil web and to stimulate the plants natural defenses. 

My reason for culturing the microorganisms found in frass is to create suppressive isolates; then colonize the rhizosphere with nonspecific fungal antagonists and initiate a systemic acquired resistance (SAR) to fortify the plant's defenses by triggering a hypersensitive response.  I will also attempt to artificially trigger SAR by spraying this homemade plant activator on the foliage in hope of growing plants highly resistant to a broad range of pathogens.

The video above shows the first step of my IMO Frass experiment.  

I will include more videos as I progress

I attempted to find other studies involving frass.  The research papers

Biological control of Sclerotinia minor using a chitinolytic bacterium and actinomycetes 

and

An Overview of Plant Defenses against Pathogens and Herbivores

were the only ones that even came close so I'm including these links for those who wish to go deeper.
The basic idea came about when I began to research Indigenous Micro Organisms - IMO and Bakashi Effective Microorganisms.  Below is a collection of video links to the material I watched
     IMO Farming part 1

Korean Natural Farming - IMO Part 1
Korean Natural Farming - IMO Part 2
Korean Natural Farming - IMO Part 3

Bryan McGrath created the series above.  I have summarized his method below.
IMO 1 - Start local indigenous micro organisms on hard cooked rice.  Cover with inoculate such as grass, bamboo or leaves.
IMO 2 - Mix 50/50 by weight with brown sugar.
IMO 3 - Mix with wheat bran and flour.  Mix 3 parts water to 1 part IMO 2. Combine this with 12 lb wheat bran and 1 cup flour till moist but not soaked.  Let compost till cool and clumped with mycillium.
IMO 4 - Mix with soil or bakashi compost.  1:1 ratio.

Another source of information comes from SQWworm Sosiety   Bryan McGrath is also featured in on this site but the methods are slightly different

http://sqworms.weebly.com/imo-indigenous-microorganisms.html

I'm basing this experiment on information from 
http://www.onfrass.com/docs/One%20sheet_Applications%20and%20Benefits.pdf
where I found this:

INSECT CHITIN–Chitin stimulates the plant’s auto-immune system to create plant secondary metabolites(PSMsor“exudates”)such asChitinase Enzyme,Terpenes, Flavinoids,Alkaloids and Amino Acids,which protect plantsfrom Pests and Pathogens–The absolute best Fungal Food for Compost Teas–Works exceptionally well with Mycorrhizae–Prevents/Kills Root Rot (fungal pathogens in the rhizosphere)–Kills Root-Feeding Nematodes and their eggs

Chitinases are enzymes that catalyze the degradation of chitin

Chitin stimulates the plant's auto-immune system to create plant secondary metabolite s (PSM s or “exudates ”) such as Chitinase Enzyme, Terpenes, Flavinoids, Alkaloids and Amino Acids, which protect plants from Pests and Pathogens
Plants often wait until pathogens are detected before producing toxic chemicals or defense-related proteins because of the high energy costs and nutrient requirements associated with their production and maintenance. This phenomenon is called systemic acquired resistance (SAR) and represents a heightened state of readiness in which plant resources are mobilized in case of further attack. Researchers have learned to artificially trigger SAR by spraying plants with chemicals called plant activators. These substances are gaining favor in the agricultural community because they are much less toxic to humans and wildlife than fungicides or antibiotics, and their protective effects can last much longer. - An Overview of Plant Defenses against Pathogens and Herbivores

My frass experiment uses the IMO method, but Effective Microorganisms are very similar.  Below are written instructions

Making Effective Microorganisms from Scratch.

Mix one cup rice with two cups water and shake.  Strain out the rice.  Cover and secure a paper towel over the top of the jar.  Leave in the dark, between 68 and 77 degrees F for five to seven days to culture the active microbes.  The mixture should smell sour.   Add 10 parts milk (about 5 quarts) to the one part strained rice wash, and let it ferment for 14 days.  The rice wash grows many microbes,  both beneficial and pathogenic.  The milk kills off everything but the lactobacillus. Strain the solids off the top of the bucket. The yellow liquid is purified lactobacillus serum.  Dilute the lactobacillus serum in a 1:20 ratio with water and add it to your compost 

Fungal Diseases

Green house pest management can be an overwhelming problem; especially in an aquaponic system.  I posted this in my other blog Chicoaquaponic.blogspot.com.  But these fungi are not limited to soil less gardens or greenhouses.



5427594
I'd like to thank Forestry Images for thier wonderfully helpful site.
With great photos to help identify various problems,  microscopic slides and petri dish samples they have made identification much simpler.

Pythium diseases

brown spot

Phytophthora blight Fusarium wilt
blue mold   powdery mildew leaf scorch sour rot
white ear rot and seedling blight of maize bitter rot and anthracnose

Jon Parr and Vlad are some of the best contributors to the aquaponic  forums.
Here's a little advice they have pasted on that I appreciate.

Link to discussion

GH (Green House) pest management has three strategies, and which is best is really open for debate.
1- intentionally low pest security, meaning wide open large screens for honey bees, pests, and pest predators. This works pretty good for lazy folks like myself, especially if you are planting beneficial plants to attract the predators. No fuss about pollination, and no big concern about sterilizing everything.
2- moderate pest security. This one is fine for new greenhouses, and light traffic GH's with cleanly guests. Once a pest gets inside, though, trouble trouble.
3- high security, meaning positive pressure and HEPA filters, thrips screening, humidity and temp control, haz-mat suits and dissinfect routines. Just the thought of all that work spoils my mood, but is probably the smartest long term plan for commercial use.

I'm a low security type guy. Address the pest directly. Mold? Increase airflow and temp, decrease humidity. Spider mites, fungus gnats, white flies, aphids? Allow predators, spray with tea, nuke them with CO2. Nasturtiums are awesome for the garden by the way; trap crop or aphids, pest predator magnets, repel white fly and spider mites. Yep. And borage, and multicropping.

 Vlad Jovanovic
Link to discussion.

You can use the 'ol 3-5% oil + 0.5% dish washing detergent remedy...works well but you have to be real careful to get as little of the concoction into your system and take measure to cover up your FT to protect from overspray. And even this low % of oil will burn pepper plants if you have any...won't damage them beyond repair or anything, just don't be freaked out by the necrotic lesions that will be left on their leaves. peppers seem especially sensitive to this type of treatment.
A better/easier/more fish safe bet might be a naturally occurring fungus called Beauvaria bassiana that will take care of a whole host of common garden pests...spider mites included (and then some). B. bassiana can be purchased under the trade names Botaniguard, Naturalis-L or Mycotrol-O the later two being ok'd by OMRI...and more importantly it is fish safe (unlike any kind of oils or most soaps).
Whatever you spray with make sure to repeat after 3 or 4 days...then again after 3 or 4 days...and then once more...since most of these sprays wont kill the eggs that they've laid...so make sure you get the bastards that have hatched...and spray the under-sides of the leaves...Good luck. Spider mites are a royal PITA.

Here is a link to another in depth discussion about Botrytis cineria and Sclerotinia sclerotiorum
Botrytis blight 
Sclerotinia rot

The Yin and Yang of Pest Control

The most important concept to remember is that weeds proliferate in unbalanced soils, and insects and diseases feed on unhealthy plants. A garden or field full of pests is not normal.
Once you know that, it’s all about implementing the steps in this book. When we stop spraying toxins, provide sufficient water, increase humus and improve the soil food web, balance soil nutrients and ensure there is proper energy in the system, pests go away. 
- Phil Nuata  (The Holistic Gardening Hardbook)

If you really want a full understanding of pathogenis response in plants An Overview of Plant Defenses against Pathogens and Herbivores provides an easy to understand yet in depth view of how plants fend for themselves.


I took my bug zapper down after finding praying mantis, and lace wings stuck to the wires.  Zappers kill indiscriminately.  I found it interesting that spiders figured out that there are a lot of bugs by the light. The webs were thick near the zapper.  It stands to reason that a high concentration of bugs will attract other beneficial insects into the killing zone as well.

Zapping the good guys is not good, and tiny insects like whitefly and aphid are probably too small to be zapped anyway.

So far my garden is doing well with nothing but compost tea.  I bought some insect frass and BT (Bacillus thuringiensis) several weeks ago, but I have not used it yet. The beneficial insects, and the good health of my plants seems to be enough so far.   I had a lot of aphids for a short while, but then the ladybugs flew in, and ate them.  It was beautiful.  I had hundreds of ladybugs come to my garden and then most of them left after the aphids were gone.  They laid a lot of eggs, and I had lots of baby ladybugs too.

insect frass contains chitin which stimulates the plant's auto-immune system to create plant secondary metabolite s (PSM s or “exudates ”) such as Chitinase Enzyme, Terpenes, Flavinoids, Alkaloids and Amino Acids, which protect plants from Pests and Pathogens
Plants often wait until pathogens are detected before producing toxic chemicals or defense-related proteins because of the high energy costs and nutrient requirements associated with their production and maintenance. This phenomenon is called systemic acquired resistance (SAR) and represents a heightened state of readiness in which plant resources are mobilized in case of further attack. Underground messaging systems also allow neighboring plants to invoke herbivore defenses before attack. Researchers have learned to artificially trigger SAR by spraying plants with chemicals called plant activators (insect frass ). These substances are gaining favor in the agricultural community because they are much less toxic to humans and wildlife than fungicides or antibiotics, and their protective effects can last much longer.

Ants can be particularly difficult but Keveen Gabet  wrote this in his article Ants – From Warship to Worship (Mexico).

Despite the few occasional bites and their compulsive leaf-cutting and seed-robbing habits, ants are wonderful allies. If you find the mother nest, you will be blessed with a mound of great compost-like soil as well as tiny gravels that will improve soil drainage. Now that’s a great bonus. They also offer long hours of entertainment; watching them fight other colonies, communicate or carry bulky items is like entering a Nat Geo documentary for a bit. As for their destructive temper, I guess all they want is food. If food it is they want, food they shall have!

Mango peels to keep my ants pacified

I now have opted for a more conscious approach and instead of making them my enemies, I have declared them worthy of my adoration. Everyday, I spread a bit of our food (fruit peels and sugary stuff like raisins for instance) close to their nest or on their way to my garden as my offering. I do it almost ritually just because it’s fun.
Overall, I call it a multilateral success as peace reigns over our little oasis once again, and they seem to have lost interest in ‘my’ share of the garden. 
--------------------------------------------------------------------------------------------

I planted quite a few beneficial plants to attract bugs.  I have asylum, nasturtium, poppy, and marigolds scattered throughout my garden.  I love to spend my time in my beautiful garden of vegetables, flowers, bees and I'm willing to let the bugs eat some of my crop knowing that there is balance.

Please be careful not to kill the pollinators. Modeled after nicotin,  neonicotinoids only sound natural and safe.

 

"Scientists studying the massive global bee die-off have unearthed a slew of evidence on the devastation across the food chain caused by the most widely-used pesticide on Earth, neonicotinoids. Once they enter the water supply, neonicotinoids wipe out dragonflies, snails and other waterborne life. The few hardy species that survive are left so toxic that they're killing birds -- and Lowe's and Home Depot are putting this toxic product right in our back yards. ... Up to a third of all honeybees vanish each winter, beekeepers are saying that we are "on the brink" of not being able to pollinate all our crops."-(Sum Of Us)
Insecticides such as Acetamiprid, Thiacloprid, Methiocarb, Abamectin, Imadicloprid are forms of neonicotinoids.

I hope everyone will go to this site  (Sum Of Us) and sign the petition 

and discourage the use of bee-poisoning neonicotinoids. 

Sevin and many other insecticides including bifenthrin, and permethrin (Eight), will kill the Aphids but also are deadly to many beneficial insects such as bees, other pollinators, and Lady Bugs that eat Aphids.

Here's some good news.  This site says that Neem Oil does not kill bees or other beneficial insects.  The insect must eat the plant in order to die.  Ladybugs and bees are left unharmed.
I have heard of people adding neem flour to thier soil and some even use neem flour as their media to ward off pests.   I have been wondering if this would destroy the beneficial organisms in the soil.  I asked the worm farm where  I buy my compost and castings to run a test, but they never did.  So I asked for a microscope for my birthday.  I should have an answer near the end of July.

According to ladybug.uconn.edu/ Insecticidal soap does not kill bees or hard bodied insects and only kills soft bodied insects when it is wet.  Unfortunatly it does kill some beneficial insects such as syrphid fly larvae and beneficial predatory mites.

Molasses offers good protection, and it will not hurt the beneficial insects.  It can also be mixed with Essential Micro Nutrient (EM) to create a health boosting shield against the insects we which to keep away.
Chamomile tea, horsetail tea, copper and sulfur products are often used for fungicides.  I have not looked to see if they are friendly towards the beneficial insects.   Milk garlic and baking soda are also used and I would imagine that they are pretty safe.

There are different strains of B.t. (Bacillus thuringiensis), each with specific toxicity to particular types of insects:
B.t. aizawai (B.t.a.) is used against wax moth larvae in honeycombs;
B.t. israelensis (B.t.i.) is effective against mosquitoes, blackflies, fungus gnats and some midges;
Most of the BT   formulations contain Bacillus thuringiensis var. kurstaki. .
B.t. kurstaki (B.t.k.) controls various types of lepidopterous insects, including the gypsy moth and cabbage looper.
A new strain, B.t. san diego, has been found to be effective against certain beetle species, Colorado potato beetle, and the boll weevil.
In order to be effective, B.t. must be eaten by insects in the immature, feeding stage of development referred to as larvae. It is ineffective against adult insects. Monitoring the target insect population before application insures that insects are in the vulnerable larval stage (9). More than 150 insects, mostly lepidopterous larvae, are known to be susceptible in some way to B.t. (5).   - Extension Toxicology Network


The package label will say for which insects the product is effective.  There are about 150 species of pest moths and butterflies that are susceptible to Bt in their larval stage, including tomato hornworm, corn earworm, cabbage looper, imported cabbageworm, and the diamondback moth.

Target pests of Bacillus thuringiensis var. kurstaki The following pests are susceptible to B.t. var. kurstaki, the most common commercially available species. Be sure to read all labels before treatment to make sure your target pest is included.
Armyworm Bagworm Cabbage looper Diamondback moth Fall cankerworm Fall webworm Gypsy moth	Imported cabbageworm Indianmeal moth Mimosa webworm Sod webworm Spring cankerworm Tent caterpillars Tomato/tobacco hornworm

Vegetable Gardener.com

It's important to learn how to identify the bugs in your garden so you know whether they are beneficial or not.   This is one of my favorite sites for insect identification. http://bugguide.net/node/view/15740

This PDF  offers many ways to protect your garden without pesticides and is a good place to start.
Insect Frass is also a great way to protect your garden and provide extra nutrients as well.  Here is more information about Frass.
or read the post I made about Frass a few days ago

Boric acid which is nontoxic to birds, fish, aquatic invertebrates, and relatively nontoxic to beneficial insects is effective in killing fire ants, spiders, cockroaches, fleas, termites, beetles, silverfish, and cockroach colonies.

Spinosad has high efficacy, a broad insect pest spectrum, low mammalian toxicity, and a good environmental profile. This is a unique feature of an insecticide, compared to others that are currently used for the protection of grain products.^[5] Spinosad is considered a natural product and approved for use in organic agriculture by numerous national and international certifications.^[8]    - Wikipedia

Spinosad is a novel insect control agent derived by fermentation of the Actinomycete bacterium, Saccharopolyspora spinosa. Spinosad controls many caterpillar pests in vines, pome fruit and vegetables (including tomatoes and peppers), thrips in tomatoes, peppers and ornamental cultivation and dipterous leafminers in vegetables and ornamentals. Application rates vary between 25 to 100 g of active substance per hectare (g as/ha) and 4.8 to 36 g of active substance per hectolitre (g as/hL) depending on the crop and target pest. It is important that plant protection products are authorized for use only in ways that do not pose an unacceptable risk of harm to honeybees. For this purpose testing was performed to enable the safety of spinosad to be evaluated. The effects of spinosad to honeybees have been extensively researched. Testing has been performed under a variety of conditions in a range of countries globally. Studies to determine the acute toxicity of spinosad under laboratory conditions were conducted to generate LD50 or LC50 values for oral and contact routes of administration. These demonstrated that spinosad was highly toxic to worker honeybees under worst case laboratory conditions and that the oral route of exposure provided the greater risk. Residue tests conducted under laboratory, semi-field and field conditions on worker honeybees foraging on treated foliage indicated that dry product residues were harmless. Therefore the effects seen in the laboratory acute toxicity tests did not translate to a more realistic exposure scenario indicating that safe use patterns for the product can be developed. Semi-field cage studies have also demonstrated that spinosad was safe to bees when applied to flowering crops during periods of bee activity. The majority of studies conducted have indicated that spinosad does not adversely affect honeybee behaviour, brood or queen. It can be concluded that spinosad when used according to the approved product label recommendations, would be safe to foraging worker bees, queen and brood. Additional levels of safety could be achieved by avoiding situations where bees would forage primarily on aphid honey dew. - Dow AgroSciences

Essentria_IC3
http://www.envincio.com/essentria/product-dload/Essentria_IC3_PIB.pdf
This product uses an Octopamine Blocker which is a lot like adrenaline to an insect.  It over excites their nervous system and kills them.  I became interested in this product when I had a severe outbreak of ants in my aquaponic green house.  While it is safe for mammals and fish I would worry about using it around crustaceans.   It is broad spectrum so you must also be careful not to kill beneficial insects like ladybugs and bees.

I used this product in my house and green house.  I did find one dead cockroach in the garage where I dumped a very large amount of Essentria_IC3 mixed at the lowest recommended strength of 1/2 oz per gallon of water.   This same ratio did nothing to the ants and aphids I wanted to kill.

I then mixed 6 oz per gallon (the maximum recommended dosage) and sprayed heavily in the green house, and on a heavy infestation of aphids on my cabbage. Once again the product failed to kill anything including the aphids which received a heavy drenching.  I waited 5 days and then mixed the Essentria_IC3 at  96 oz per gallon.  Sixteen times the recommended strength.   The good news is it did not harm the fish and it did kill both the aphids and the ants.  The bad news is it destroyed many of my plants.  It may be a better herbicide than it is a pesticide.

I would not recommend Essentria_IC3.  It's was ineffective in my green house and garden.  The smell is horrid, and required that I air my house out for two days when mixed at the lowest ratio.
Diatomaceous earth (DE) is non toxic and far better than many poisons.  But it kills all bugs including bees, and other beneficial insects so it's not always the best choice.
It's only effective until it becomes wet.  This is a really good thing because it allows you to use DE for a specific period of time.  Bees tend to come around in the morning and afternoon.  Dusting DE in the evening will avoid getting it on the bees.  But you still risk killing many other beneficial insects.
DE kills due to its sharp edges, and will only kill the insects that come in contact with it so it will not kill the other bees in a hive.  It's safe for humans and other mammals, but it would not be my first choice because it's an indiscriminate killer.
For more information http://www.wormfarmingrevealed.com/diatomaceous-earth-and-bees.html

Make Your Own Bug Sprays

 Nicotine -  Extremely toxic to insects. Nicotine tea is short lived, retaining its toxicity for only a few hours after spraying. It is relatively nonhazardous to bees and lady beetles because of its short persistence, but timing is required.
Pyrethrum - The dried, powdered flowers of the pyrethrum daisy, Tanacetum cinerarifolium, were used as early as 1880 to control mosquitoes.
Capsaicin - Black pepper, chili pepper, dill, ginger, paprika, and red pepper all contain capsaicin, a compound shown to repel insects.
Herbal Sprays - Extracts of Hyssop, Rosemary, Sage, Thyme,  White Clover, Wormwood,  Nasturtiums, Catnip, Chives, Feverfew, Marigolds, or Rue can be used.
Garlic Oil - Combine with mineral oil and pure soap
Tomato Leaf - Soak chopped leaves. Contains toxic compounds called alkaloids and attracts natural pest enemies.Alcohol Sprays - Alcohol sprays work on aphids, mealy bugs, scale insects, thrips and whiteflies
 For more information about these homemade sprays - Comfy Country Creations

More Links:
Sierra Club - Imidacloprid Fact Sheet
The Basics of Organic Gardening in 15 minutes
Key to Major Beneficials and Pests


Update 5/26/13 Some of my cucumbers leaves are showing damage.  I could not find the pest, but I suspect a worm, so I sprayed BT kurstaki.

Killing bees and birds

This is killing off the bees and taking out birds. So why are @HomeDepot and @Lowes selling it?
Find out - Click Here > http://bit.ly/Yc88xq  via @Sum_of_Us

 

Acetamiprid, Thiacloprid, Methiocarb, Abamectin are forms of neonicotinoids

Helene sells called TriStar with Acetamiprid.  
Lowes sells Provado with Thiacloprid.

The insects eat the plant which absorbs the neonicotinoids then birds die from eating the insects.
Bees absorb it directly as they pollinate the plants.

Here is a list to avoid:
http://www.pan-uk.org/home-garden/list-of-home-and-garden-pesticides-containing-neonicotinoids

Eco-friendly solutions for garden pest-control

Chico News & Review - Pest patrol - Sustainability - Green - May 9, 2013

www.newsreview.com

Environmentally friendly ways to control garden pests.

The Soil Web

This is really interesting stuff!   Most of what I have written was learned from reading Teaming with Microbes by Lowenfels & Lewis.  It began as notes I was taking as I read the book. I think the book is a masterpiece.

<<<==================>>>

 The Soil Web

Plants secrete chemicals made of proteins and carbohydrates, called exudate through their roots.

The dark spots are bacteria.  The less defined areas are the excudates emanating from the root on the right

Rhizoshere

The excudates are soluble sugars, amino acids and other compounds secreted by roots.  They attract specific beneficial bacteria and fungi in the rhizoshere which looks like jam under a microscope.
Bacteria, fungi, nematodes, and protozoa and even some larger organisms compete for the excudates, water, and minerals within the rhizoshere.

Nutrients which would otherwise wash out of the soil are retained by these organisms which cling to the rhizoshere. .
Both good, and bad bacteria compete for the excudates, but if the soil is healthy good organisms such as fungi that produce inhibitory compounds such as penicillin and streptomycin prevent disease from entering the plant.  Also Mycorrhizal fungi will be present to protect the roots, and deliver water, phosphorus, and other nutrients.

Nitrogen is a basic building block of amino acids. 
In  general perennial trees and shrubs prefer fungal dominated soil while annuals, grasses and vegetables prefer bacteria based soils.
The key is to encourage the type of soil (fugal or bacteria) to thrive so that the plants get the type of nitrogen they they prefer. 

It has become common practice to add "-icides" which are an irritant to the worms. These poisons kill, or drive the worms away.  On top of that, the common practice of adding salt based chemical fertilizers rather than replacing organic material deprive the worms of food, and tilling crushes, and kills any worms and arthropods that might remain.  The soil now lacks life, and becomes compacted. Water no longer brings oxygen down into the soil, and pathogens establish themselves.

Healthy soil will contain between 20 to 30 thousand different species in just one teaspoon of good soil.  Each group must be kept in balance.  Nature does a good job of this but agricultural chemicals can kill off entire groups and decimate the balance, which in turn removes food supplies for other groups.

Jeff Lowenfels Soil Food Web Lecture

Letters are used to describe the soil layers   The 'O' layer lies above the 'A' layer.  Several other horizons lie below until bedrock is reached, but  'O and 'A' are the only two layers gardeners are concerned with.  .    The 'O' horizon is broken down further into 'Oi', 'Oe' and 'Oa' depending on the condition of decomposition the organic mater is in .  The specific plant source of organic material can still be identified in 'Oi' .  In 'Oe' the organic material can only be identified as plant, and finally 'Oa' has decomposed so much that identification is not possible.
The roots grow in the rich humus of the A layer which is  full of organic matter, and biological activity which has leached down into it from the 'O' layer above.  It's important that these layers have a good mixture of air, water, minerals and organic matter. Humus or humified organic matter is complex organic compounds that remain after many organisms have used and transformed the original material. Humus is not readily decomposed because it is either physically protected inside of aggregates or chemically too complex to be used by most organisms. Humus is important in binding tiny soil aggregates, and improves water and nutrient holding capacity.


Minerals can influence the color of soil.  Red and yellowish tints are an indication of iron,  purple - black indicates manganese.  Gray can indicate a lack of organic matter, and an anaerobic condition due to the microbes having converted the iron to Fe2+.   Organic matter produces much stronger coloring agents as it decomposes, but in an anaerobic soil it can also provide food for anaerobic bacteria that reduce iron and manganese. Therefore gardeners are looking for dark soils the color of coffee.

There are three categories of soil texture: The categories are a description of how the particles sizes feel to your touch, not the actual mater.  Sand which is gritty, silt which is like flour and clay is slippery.  An ideal garden soil texture will have all three in approximately equal amounts. This is called loam.  Loam has the ability to drain and draw air down into the soil like sand while holding water and nutrients like clay and silt.

An ideal ratio would be about 30 to 50% sand, 30 to 50% silt, 20 to 30% clay and 5 to 10% organic material.  You can easily test you own soil by adding a tablespoon of water softener to 2 cups of water and a sample of your soil.  Shake and let stand for 24 hours then compare the stratification.  Sand will settle to the bottom, silt will form the next layer and then clay will finally settle leaving the organic mater to float for a while at the top.  With this knowledge you will be able to adjust your soil as required.

Nematodes may be useful indicators of soil quality because of their tremendous diversity and their participation in many functions at different levels of the soil food web. Several researchers have proposed approaches to assessing the status of soil quality by counting the number of nematodes in different families or trophic groups.* In addition to their diversity, nematodes may be useful indicators because their populations are relatively stable in response to changes in moisture and temperature (in contrast to bacteria), yet nematode populations respond to land management changes in predictable ways. Because they are quite small and live in water films, changes in nematode populations reflect changes in soil microenvironments.

Nematodes

Polysaccharides produced by worms, fungus, and bacteria stick the aggregates of the soil together, and make it easier for the soil to hold capillary water and soluble nutrients. This is the type of soil that will support soil biology, giving it the ability to withstand floods,  drought, freezing and animal traffic.

Small particles of clay and humus carry positive electrical charges call ions.  Positive ions are called cations and negative charges are called anions. The positive ion (cations) - pronounced as 'CAT Ion' of humus and clay attract the negative ions (anions) of calcium (Ca++),  potassium (K+), sodium (Na+), magnesium (mg++), iron (Fe+), ammonium (NH4+), and hydrogen (H+) so strongly that very little remains in solution.  The nutrients are held in clay and humus where roots exchange (H+) cation for a nutrient cation.

There are also anions of chloride (Cl-), nitrate (NO3-), sulfate (SO4-) and phosphate (PO4-) in the soil as well.  Since these are repelled by the humus and clay cations they are easily leached away.

Plant root hairs also have cations which are exchanged for the cations in the clay and humus.  The root hairs exchange one (H+) for every nutrient cation absorbed.  This occurs at the cation exchange site.  The Cation Exchange Capacity (CEC) is a measurement of how many exchange sites there are in the soil.  Higher CEC measurements indicate that the soil can store large amounts of nutrients, which is why gardeners like a high CEC.  But the clay and humus which give the soil this quality also prevents good drainage and aeration so a  mixture with good soil texture is important.

Each cation exchange, as well as some fungal and bacterial exchanges effect the pH of the soil.  Knowing the pH is important because different microbes prefer different soil pH and depending on the plant certain microbes may be required for nutrient exchange.

Bacteria come in two basic types.  Anaerobic which lives without oxygen and produces offensive odors, and aerobic which lives with oxygen and produces pleasant fresh odors.  Bacteria are responsible for recycling carbon, sulfur, and nitrogen.  CO2 is a by product of aerobic bacteria, and sulfur is recycled by anaerobic bacteria. 

Soil nutrients occur in two forms: inorganic compounds dissolved in water or attached to minerals and organic compounds part of living organisms and dead organic mater.  Bacteria, fungi, nematodes, and arthropods are always transforming nutrients between these two forms.  When they consume inorganic compounds to construct cells, enzymes, and other organic compounds needed to grow, they are said to be "immobilizing" nutrients.  When organisms excrete inorganic waste compounds, they are said to be :mineralizing" nutrients.

Free-living nematodes can be divided into four broad groups based on their diet.

• Bacterial-feeders consume bacteria.
• Fungal-feeders feed by puncturing the cell wall of fungi and sucking out the internal contents.
• Predatory nematodes eat all types of nematodes and protozoa. They eat smaller organisms whole, or attach themselves to the cuticle of larger nematodes, scraping away until the prey’s internal body parts can be extracted.
• Omnivores eat a variety of organisms or may have a different diet at each life stage. Root-feeders are plant parasites, and thus are not free-living in the soil.[1]

Nitrogen found in the atmosphere can not be used directly by plants. It must be 'fixed' through a process called nitrification where aerobic bacteria combine nitrogen with either oxygen or hydrogen to form  nitrite (NO2-), and eventually nitrate (NO3-) ions from the ammonium (NH4+) waste of protozoa, and nematodes which consume other bacteria and fungi. [1] This is an example of mineralization.

Nitrification produces an acidic pH.  When oxidation occurs, an electron is lost, releasing energy that is used by the bacteria.   Nitrifying bacteria do not generally like low pH, but fortunately other bacteria called denitrifying bacteria convert nitrogen salts created by the nitrification process back into nitrogen N2 which returns to the atmosphere.  The roots take up negatively charged anions (H+) exchanging hydroxy (OH-) anions.  This also helps to return the pH to a higher level.

Hydrogen is the root's currency. They sell OH- for H+, and then exchange H+ for nutrient cations.  Even microorganisms carry their own charges, and are also influenced by the anions an cations of the roots and soil.

Bacteria fall into four functional groups. Most are decomposers that consume simple carbon compounds, such as root exudates and fresh plant litter. By this process, bacteria convert energy in soil organic matter into forms useful to the rest of the organisms in the soil food web. A number of decomposers can break down pesticides and pollutants in soil. Decomposers are especially important in immobilizing, or retaining, nutrients in their cells, thus preventing the loss of nutrients, such as nitrogen, from the rooting zone.[1]

A second group of bacteria are the mutualists that form partnerships with plants. The most well-known of these are the nitrogen-fixing bacteria. The third group of bacteria is the pathogens. Bacterial pathogens include Xymomonas and Erwinia species, and species of Agrobacterium that cause gall formation in plants. A fourth group, called lithotrophs or chemoautotrophs, obtains its energy from compounds of nitrogen, sulfur, iron or hydrogen instead of from carbon compounds. Some of these species are important to nitrogen cycling and degradation of pollutants.[1]

Bacteria live in a matrix of sugars, proteins, and DNA called Bio-film or Bacteria Slime which helps sustain them through drought and attack from antibodies and other bacteria.  Bacteria prefer the vicinity of root hairs because of the available food from the excudates.  The nutrients within the bacteria are unavailable to the plants until the bacteria die and so goes the cycle.  Bacteria feed on the excudates in the root zone, absorbing nutrients which will be later be made available to the plants when they die.  There are also Mutualistic Bacteria which live on the root nodules of peas and beans.  These bacteria trade amino acids containing nitrogen for carbohydrates without the need for the bacteria to die.

Pathogenic bacteria often produce toxic alcohols if the soil has poor texture and drainage.  They can cause citrus canker, diseases of potatoes, melons and cucumbers and fire-blight of pears, and apples, galls and tumors, root rot on onion, leaf curl and black spot on tomatoes, but beneficial bacteria compete strongly for food and starve out pathogenic bacteria.  By keeping your soil alive you can avoid these problems, but intervening with "-icides" will kill the good bacteria as well, leaving you with dead soil.

Certain strains of the soil bacteria Pseudomonas fluorescens have anti-fungal activity that inhibits some plant pathogens. P. fluorescens and other Pseudomonas and Xanthomonas species can increase plant growth in several ways. They may produce a compound that inhibits the growth of pathogens or reduces invasion of the plant by a pathogen. They may also produce compounds (growth factors) that directly increase plant growth.  [2]
These plant growth-enhancing bacteria occur naturally in soils, but not always in high enough numbers to have a dramatic effect. In the future, farmers may be able to inoculate seeds with anti-fungal bacteria, such as P. fluorescens, to ensure that the bacteria reduce pathogens around the seed and root of the crop.[2]

Natural insecticides such as spinosin A & D,  and bacillus thuringiensis grow in healthy soil.  Nicotine and Pyrethrum (not to be confused with pyrethroids), are also naturally occurring insecticides produced by the plants.  I mention these because there are many biopesticides in and outside of the soil which can control pests naturally.   But 'natural insecticide' does not mean harmless.  Further information about organic pest management can be found at these links
http://anrcatalog.ucdavis.edu/pdf/7251.pdf
http://en.wikipedia.org/wiki/Category:Plant_toxin_insecticides 

The roll fungus plays in soil is astounding.  Saprophytic fungi decompose dead organic matter while mycoohrhiza fungi associate with the plant roots exchanging energy and nutrients.  Bacteria are good at breaking down the sugars in organic mater, but saprophytic fungi can break down harder mater such as chitin and bark.  We are unable to see most of the fungal hyphae, but it can branch out as fast as 40 micrometers per second extending it's network over relatively large areas, and can extend down deeper than bacteria.  The fungal hyphae absorb nutrients very much like bacteria, but they also have the ability to locate and reach out to these nutrients.  Fungi even have the ability to attract and suck the nutrients out of unsuspecting nematodes.  Organic mater is broken down into compounds, and ingested by acidic substances leaked out of their hyphal tips.  The fungal network transports nutrients, and water long distances to the roots which attract the fungus with exudate. 
When the fungus dies, it too just like bacteria, make the nutrients it previously absorbed available to the plant roots.  It also leaves behind long tunnels which bacteria, air, and water can move through. 

Fungi release nitrogen as ammonium (NH4+) or nitrite (NO3-) and other nutrients as part of their waste, which feeds the nitrifying bacteria.  But the acidic emzimes produced by the fungi lower the pH and as we know nitrifying bacteria prefer a pH over 7.  Without the nitrifying bacteria the ammonium (NH4+) and nitrite (NO3-) will not be converted.  This is not good for most vegetables, but in  general perennial trees and shrubs prefer fungal dominated soil while annuals, grasses and vegetables prefer bacteria based soils. You may have noticed that mycillium is often found in forest soil.

Mycorrhizae fungus are very fragile.  Chemicals, compaction, roto tilling and double digging destroy the fungal hyphae.

Fungal Hyphae

There are two kinds of mycorrhizae.  Ectomycorrhizal which grow close to the surface and endomycorrhizal which penetrate and grow inside the roots as well as extend outward.  This is preferred by most vegetables.  A major function of Mycorrhizae fungus is to transport phosphorus back to the plant.  Copper, calcium, magnesium zinc and iron are also moved back to the plant.  But just as important; the fungus also unlock and change the ion state of these elements so that the nutrients are soluble and available to the plant.

There are hundreds of endophytic fungal species.  Some are beneficial others are not, but nearly all plants are infected.  Endophytic fungal can occasionally transport nutrients between more than one plant.   Some produce toxins that kill pests, limit seed production, increase the rate of seed germination, cause resistance to disease, or speed the decay process after a plant has died.  Others are pathogenic such as those that cause powdery mildew, rust fungus, or fusarium wilt on tomatoes which can lay dormant in the soil for more than a  decade.  The first indication of fusarium wilt is yellow leaves starting at the bottom.  Gardens are filled with fungus that create vitamins,  antibodies, affect pH,  kill bacteria and nematodes as well as those that destroy a garden.


Fungal-dominated soils (e.g. forests) tend to have more testate amoebae and ciliates than other types. In bacterial-dominated soils, flagellates and naked amoebae predominate. In general, high clay-content soils contain a higher number of smaller protozoa (flagellates and naked amoebae), while coarser textured soils contain more large flagellates, amoebae of both varieties, and ciliates. [1]

Protozoa are much larger than bacteria and nematodes which they feed up on.  Protozoa are an important part of soil because worms eat protozoa and when protozoa die they too provide nutrient and food for the bacteria.  The soil is a web of unending transformation.

Nematode

Nematodes transport minerals fungi and bacteria.   They are larger than protozoa and are not be able to deliver nutrients to the plant roots if the soil is compacted. Most nematodes in the soil are not plant parasites. Beneficial nematodes help control disease and cycle nutrients.

Nutrient cycling. Like protozoa, nematodes are important in mineralizing, or releasing, nutrients in plant-available forms. When nematodes eat bacteria or fungi, ammonium (NH4+) is released because bacteria and fungi contain much more nitrogen than the nematodes require.
Grazing. At low nematode densities, feeding by nematodes stimulates the growth rate of prey populations. That is, bacterial-feeders stimulate bacterial growth, plant-feeders stimulate plant growth, and so on. At higher densities, nematodes will reduce the population of their prey. This may decrease plant productivity, may negatively impact mycorrhizal fungi, and can reduce decomposition and immobilization rates by bacteria and fungi. Predatory nematodes may regulate populations of bacterial-and fungal-feeding nematodes, thus preventing over-grazing by those groups. Nematode grazing may control the balance between bacteria and fungi, and the species composition of the microbial community.
Dispersal of microbes. Nematodes help distribute bacteria and fungi through the soil and along roots by carrying live and dormant microbes on their surfaces and in their digestive systems.
Food source. Nematodes are food for higher level predators, including predatory nematodes, soil microarthropods, and soil insects. They are also parasitized by bacteria and fungi.
Disease suppression and development. Some nematodes cause disease. Others consume disease-causing organisms, such as root-feeding nematodes, or prevent their access to roots. These may be potential biocontrol agents.[1]

Arthropods range in size from microscopic to several inches in length. They include insects, such as springtails, beetles, and ants; crustaceans such as sowbugs; arachnids such as spiders and mites; myriapods, such as centipedes and millipedes; and scorpions.[1]  Arthropods transport fungi and bacteria while shredding up to 30% of the organic mater on temperate zone forest floor.

Springtail

Arthropods can do damage to crops, but they are a valued member of the soil web. Most live on the surface, but others such as Rugose harvester ants ( Pogonomyrmex rugosus) are scavengers rather than predators. They eat dead insects and gather seeds in grasslands and deserts where they burrow 10 feet into the ground. Their sting is 100 times more powerful than a fire ant sting, but they help mix and aerate the soil while adding organic matter. 

Mites

Termites and ants bring organic mater down into the soil, and in tropical areas they mix more soil than worms.  Termites digest their food with the help of pathogenic archea creating methane and are a major contributor to greenhouse gas. Their populations are very important to the soil web.

Although the plant feeders can become pests, most arthropods perform beneficial functions in the soil-plant system.
Shred organic material. Arthropods increase the surface area accessible to microbial attack by shredding dead plant residue and burrowing into coarse woody debris. Without shredders, a bacterium in leaf litter would be like a person in a pantry without a can-opener – eating would be a very slow process. The shredders act like can-openers and greatly increase the rate of decomposition. Arthropods ingest decaying plant material to eat the bacteria and fungi on the surface of the organic material.
Stimulate microbial activity. As arthropods graze on bacteria and fungi, they stimulate the growth of mycorrhizae and other fungi, and the decomposition of organic matter. If grazer populations get too dense the opposite effect can occur – populations of bacteria and fungi will decline. Predatory arthropods are important to keep grazer populations under control and to prevent them from over-grazing microbes.
Mix microbes with their food. From a bacterium’s point-of-view, just a fraction of a millimeter is infinitely far away. Bacteria have limited mobility in soil and a competitor is likely to be closer to a nutrient treasure. Arthropods help out by distributing nutrients through the soil, and by carrying bacteria on their exoskeleton and through their digestive system. By more thoroughly mixing microbes with their food, arthropods enhance organic matter decomposition.
Mineralize plant nutrients. As they graze, arthropods mineralize some of the nutrients in bacteria and fungi, and excrete nutrients in plant-available forms.
Enhance soil aggregation. In most forested and grassland soils, every particle in the upper several inches of soil has been through the gut of numerous soil fauna. Each time soil passes through another arthropod or earthworm, it is thoroughly mixed with organic matter and mucus and deposited as fecal pellets. Fecal pellets are a highly concentrated nutrient resource, and are a mixture of the organic and inorganic substances required for growth of bacteria and fungi. In many soils, aggregates between 1/10,000 and 1/10 of an inch (0.0025mm and 2.5mm) are actually fecal pellets.
Burrow. Relatively few arthropod species burrow through the soil. Yet, within any soil community, burrowing arthropods and earthworms exert an enormous influence on the composition of the total fauna by shaping habitat. Burrowing changes the physical properties of soil, including porosity, water-infiltration rate, and bulk density.
Stimulate the succession of species. A dizzying array of natural bio-organic chemicals permeates the soil. Complete digestion of these chemicals requires a series of many types of bacteria, fungi, and other organisms with different enzymes. At any time, only a small subset of species is metabolically active – only those capable of using the resources currently available. Soil arthropods consume the dominant organisms and permit other species to move in and take their place, thus facilitating the progressive breakdown of soil organic matter.
Control pests. Some arthropods can be damaging to crop yields, but many others that are present in all soils eat or compete with various root- and foliage-feeders. Some (the specialists) feed on only a single type of prey species. Other arthropods (the generalists), such as many species of centipedes, spiders, ground-beetles, rove-beetles, and gamasid mites, feed on a broad range of prey. Where a healthy population of generalist predators is present, they will be available to deal with a variety of pest outbreaks. A population of predators can only be maintained between pest outbreaks if there is a constant source of non-pest prey to eat. That is, there must be a healthy and diverse food web.
A fundamental dilemma in pest control is that tillage and insecticide application have enormous effects on non- target species in the food web. Intense land use (especially monoculture, tillage, and pesticides) depletes soil diversity. As total soil diversity declines, predator populations drop sharply and the possibility for subsequent pest outbreaks increases.[1]

Earthworms shred debris so other organisms can digest it.  they make the soil more porous, increase water retention, fertility and add to the organic mater of soil. while the inch their way through hard soil they move nutrients,  transport microbes, and create pathways for roots,  leaving  behind a slime which helps to bind soil particles together.  Why then would a gardener roto-til the soil killing the worms that were already breaking up the soil?  Then add fertilizers and pesticides which either kill what ever worms remain or drive them away.  If you have worms - chances are you have healthy soil full of organic matter, bacteria, archea, fungi, protozoa, nematodes and arthropods.  A healthy soil wed will provide your garden with all that it requires.

I know this is hard to believe, but even moles and snails are beneficial.  Moles aerate the soil and move smaller organisms great distances.  Snails accelerate decomposition, aerate the soil, leave slime behind that binds particles of soil and as are all creatures they too leave nutrients behind when they die.  The snails you encounter above ground are only a small percent of the total population, and they are not exclusively after your crop.  They consume more than just your lettuce.  Slugs and snails eat fungi, algae, lichens, and rotting organic mater.  In a healthy soil web they will be kept in control by snakes, lizards, spiders, and birds.  In return these predators will also keep other pests under control, and help spread fungi, and bacteria.

Predators like centipedes, spiders, ground-beetles, scorpions, skunk-spiders, pseudoscorpions, ants, and some mites  eat crop pests, and some, such as beetles and parasitic wasps, have been developed for use as commercial biocontrols. 

And lastly here is a strange fact:
Cicada  live underground for 17 years before emerging, The nanopattern  on their wings protect them from bacteria.  

Further information can be found at:
A Review on Beneficial Effects of Rhizoshpere Bacteria on Soil Nutrient Availability and Plant Nutrient Uptake
The Soil Food Web - Tuning in to the World Beneath Our Feet by Mary-Howell R. Martens
Soil Beneficial Bacteria and Their Role In Plant Growth Promotion a Review


Experts in this field are:

       Elaine Ingham, Ph.D  -  www.soilfoodweb.com

       Dr. Joyce Loper, of the USDA Agricultural Research Service

References:
http://soils.usda.gov/education/resources/lessons/color/ 
Teaming with Microbes by Lowenfels & Lewis. 

1. http://soils.usda.gov/sqi/concepts/soil_biology/bacteria.html
2. BUG BIOGRAPHY: Bacteria That Promote Plant Growth By Ann Kennedy, USDA Agricultural Research Service, Pullman, WA