Monday, February 25, 2013

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

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.

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 

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.

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.
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. 

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  -
       Dr. Joyce Loper, of the USDA Agricultural Research Service

Teaming with Microbes by Lowenfels & Lewis. 

2. BUG BIOGRAPHY: Bacteria That Promote Plant Growth By Ann Kennedy, USDA Agricultural Research Service, Pullman, WA

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