What You Should Know About Soils

What you should know about soils(updated March, 2017)

Soil is more than sand, silt, and clay with some small amount of organic matter.  You may have 3 inches of clay over caliche, or 12 inches of blackland clay, or 5 feet of sand over hardpan. Whatever you have, soil is teaming with life.

Experts estimate that a tablespoon of forest soil contains 6 billion microorganisms consisting of 75,000 species of bacteria, 25,000 species of fungi, 1,000 species of protozoa, and 100 species of nematodes.  And that is not a typo; that is number of species.

James Urban in Up By Roots uses a cup of soil (that’s a handful for me) and has numbers in the billions;    200 billion bacteria, 100,000 meters of fungi (that’s about 60 miles!), 20 million protozoa, 100,000 nematodes, 50 micro arthropods.  That’s not much soil to contain such mind boggling numbers. The numbers are so large, so extreme; I do not think they register with most of us.  It’s hard to imagine how small you have to be to have 200 billion in a handful of soil.

Under good conditions bacteria have the ability to multiply or divide every 20 minutes.  They could quickly overwhelm the soil unless billions of them were consumed every hour.  A protozoa can consume 10,000 bacteria a day and there are 20 million protozoa in a handful of soil.  Nematodes eat bacteria, some protozoa, and a lot of fungi.  Arthropods eat all of the above. Fungi consume nematodes, decompose the bodies of whatever dies, decompose organic matter, and release nutrients from soil particles and rock.  Bacteria also decompose organic matter and release nutrients from soil and rock.  All are completely dependent upon carbon which can only be supplied by plants.

This is the soil food web.  The entire process protects nutrients from leaching out of the root zone of plants by securing nutrients within the bodies of microbes.  Plants and trees are very particular about the nutrients they absorb and prefer nutrients in a form that has been manipulated by microorganisms.  The nutrient needs to be consumed by a bacteria that is then consumed by a protozoa or nematode and then pooped out in the rhizosphere in ion form. The rhizosphere is a small zone of intense biological activity about 2mm wide (1/10th inch) around a root.  Only then is the nutrient in a form that the plant root can absorb.  So bacteria put out enzymes that release nutrients that they absorb. A protozoa consumes the bacteria, uses what it needs and releases the leftovers which have been converted into a form plants can use.  If the waste is released in the rhizosphere, the expanding root is able to pick it up thru diffusion.

In exchange, the plant provides carbon sugars it has produced during photosynthesis.  About 40% of what a tree produces in its leaves is leaked out thru roots to nourish the bacteria and fungi around those roots.  That is a lot of product being leaked, an indication of how much our trees depend upon the micro soil food web.  The bacteria depend upon their sugar daddy and crowd in on the expanding root like pigs at a feeding trough, forming a physical barrier that excludes bad bacteria.  When things are healthy, the bad guys do not have access to the root or to the sugars. When things are right, the good guys out compete the bad guys, limiting the numbers that could cause trouble.

Fungi can also form a physical barrier around a root, so thick that nematodes and other bad guys are excluded. Many of these fungi are mycorrhizae fungi that are attached to the root or have structures inside root cell outer walls.  The tree provides carbon sugars to the mycorrhizae in exchange for water and nutrients, especially phosphorus.  Fungal hyphae can be 1/60th the size of an expanding root and have the ability to get water and nutrients from very small pore spaces in the soil.  Mycorrhizae fungi are able to deposit water and nutrients directly into the plant root where the water and ions move through a cell membrane into root cells.

Fungi eat or consume nematodes.  Some form snares with their hyphae, put out a nematode attractant, and close the snare when a nematode enters the trap. They then grow a special structure that penetrates the sightless worm to consume the groceries.  Other fungi produce a poison that kills the microscopic worm when the toxin touches its mouth. Some use glue to glue trap the worm.

And then there are the arthropods (mites). They are the big guys in this micro world, eating fungi and nematodes and protozoa. And all these guys are pooping nutrients in forms that plants can use. Many of these waste products get picked up and consumed enough times in this soil food web to become fairly stable compounds which are how humates are formed.

Trees and plants are completely in charge of this system.  They have the ability to change the sugars they provide to stimulate certain bacteria or fungi according to their needs.  They change the sugars they produce by season, by temperature, and by moisture levels.  If they need iron, they produce a sugar to stimulate the fungus or bacteria that can provide that need.  Low on water and they stimulate the mycorrhizae fungi to bring in more water.

Bacteria could easily be washed away so they glue themselves to soil particles.  They use organic glues produced from the sugar compounds supplied by plants. These glues are similar to the ones produced by the bacteria in your mouth that cause morning mouth and tartar.  Clay particles tend to be rod shaped and bacteria can glue these end to end forming odd shaped structures that can resemble a snow flake.  This is the smallest soil aggregate and it protects the bacteria and provides space for the slow movement of air and water.  In sandy soils bacteria form cup like aggregates which hold water.

Fungi need to protect their reproductive structures from grazing arthropods, so they weave or glue several of these bacterial soil aggregates together and hide their fruiting structures inside. The glue they use is called glomalin and it is responsible for about 33% of the carbon found in soil when mycorrhizae fungi are present. This forms a larger soil aggregate, still too small to see with anything other than a high powered microscope.  Millions of these are formed within a handful of soil and they are an important, critical component of soil structure.  The movement of nematodes and arthropods create small passages that also provide for the slow movement of air and water.  These are the aggregates we destroy with compaction, plowing, tilling, and double spading our gardens.  Once these small aggregates are eliminated, water or air will not pass through.  If you want your soil to be healthy, you should not see it very often.  Keep your soil covered with plants and undisturbed.

Trees and their roots can get lazy.  When we provide nutrients to plants in forms they can use with very little biological activity, the tree will reduce the exudates it releases, which reduces the population of the good guys and can give the bad guys access to our plants.  It makes plants dependent upon chemical fertilization.  Fertilizers with high salt content (quick release and water soluble) can desiccate bacteria and fungi and can irritate worms causing them to leave the area.

We need to regard soil as a complex system of living organisms and seriously think about becoming microbe farmers, like the trees in a climax forest.  With the exception of pH, the physical properties of soil are not nearly as important to a gardener or arborist as the invisible living microbes occupying the soil. Your top priority in caring for soil should be to protect and preserve the soil food web.

This article was based on the incredible work of Dr. Seuss in his landmark soils manual, Horton Hears a Who with help from Up By Roots by James Urban, The Soil Will Save Us by Kristin Ohlson, Teaming With Microbes by Jeff Lowenfels and Wayne Lewis, the Certified Arborist Study Guide, Teaming With Nutrients by Jeff Lowenfels, and Teaming With Fungi by Jeff Lowenfels.

David M. Vaughan
Certified Arborist TX 0118
Member American Society of Consulting Arborists
Organic Certified, Texas Organic Research Center

Pruning 101

Hover your mouse over highlighted words for useful definitions or links.

Pruning 101

PRUNING, when properly performed, is beneficial and can reduce the risk of stem and branch failure; provide clearance for structures, vehicles, and pedestrians; improve health and appearance; and improve views.  Improper pruning techniques are harmful for a tree’s health, vigor, stability, and appearance.  A tree that is not pruned, or left natural, can develop low limbs, co-dominant stems, defects such as included bark, and accumulation of dead branches.

Before pruning, determine the reason and objectives that should result.  For example, young trees, trees twenty-five years or younger, are pruned using different objectives than mature tree (trees older than twenty-five years).  On average, young trees should be pruned about seven times during their first twenty-five years after planting.

Remember, when pruning Oak trees you must paint your cuts, this includes all wounds any size, at anytime during the year!  This rule applies for all species of Oak and to wounds made, for example, from a weed eater or lawn mower.  Any latex based paint works well, the color doesn’t matter.


I. Pruning Young Trees

The objectives for pruning young trees are to: 

  • Establish and develop one dominant leader
  • Space main, scaffold limbs
  • Keep low, non-permanent branches small
  • Select lowest main scaffold branch
  • Prevent all branches from growing larger than half the trunk diameter
  • Maintain a live crown ratio of greater than 60%

Please Note: Prior to planting your tree, establish the root flare of your tree to ensure it is planted at grade and that there are no girdling roots present.  It is important to visually inspect the root flare of your tree annually and at each stage of pruning to ensure the root flare remains visible and that no girdling roots have developed.

First Pruning – Pruning at Planting: Trees that are less than four inches in diameter do not have any permanent branches.  It will take many years for the permanent branches to develop.  Shorten or remove all branches competing with the one leader that will make the best main stem.  Remove broken, cracked, damaged or dead branches.  Do not remove more than twenty-five percent of the live foliage at planting.

Second Pruning – Two Years After Planting: At this point, there still may not be any permanent branches, especially on trees less than four inches in diameter.  In order to establish a dominant leader, shorten or remove all competing leaders and branches four inches in diameter or larger within twelve inches of the largest diameter branches in the top half of the tree.  Shorten, or reduce, low, vigorous branches to improve clearances.

Third Pruning – Four Years After Planting: Most branches are temporary even four years after planting and will eventually be removed from the tree.  Shorten or remove any leaders competing with the dominant leader you have selected.  Reduce or remove low vigorous branches for clearances.  Continue to space upper canopy branches about twelve inches apart and reduce or remove branches in between.  There should be only one large branch per node.  If limbs are clustered, or have more than one branch per node, select the one branch that will remain and shorten or remove the competing branches.  Do not remove more than thirty-five percent of the live foliage.

Fourth Pruning: Eight Years After Planting: Shorten or remove any leaders competing with the dominant leader you have selected.  Select the lowest permanent branch and shorten any branches below this limb to reduce their growth.  Branches below the lowest permanent branch should be removed when they are about half the size of the trunk and after the bark in that area of the trunk has become thick and grooved, or once a branch bark ridge has been established.  Continue to space upper canopy branches at twelve to eighteen inches apart and reduce branches in-between.  The goal is to have only one branch per node, no clustered branches.  Do not remove more than twenty-five percent of the live foliage.

Fifth Pruning – Fourteen Years After Planting: Shorten or remove leaders competing with the dominant leader.  Select several permanent scaffold branches and reduce branches within eighteen to thirty-six inches of these permanent branches.  Shorten or remove branches below the permanent scaffold branches.

Sixth Pruning – Twenty Years: Shorten or remove leaders competing with the dominant leader.  Continue to identify permanent scaffold limbs and shorten branches that are between these branches, remember the goal is to have one branch per node.  Reduce or remove branches below the first permanent scaffold branch.

Seventh Pruning – Twenty-five Years: Perform the same procedures as the previous two prunings.

These seven pruning sessions accomplished within the first twenty-five years after planting will aid trees in developing good structure, enabling them to cope with high winds and most other stresses. Proper planting and good irrigation until the tree is established may allow you to prune less frequently.


Before cut After cut

II.  Pruning Mature Trees

Mature trees are usually pruned to reduce risk of failure and to provide clearances from structures and through-ways.  Occasionally mature trees need to be pruned to allow more light to the ground and for the health of the tree.  Ball moss removal is not pruning and should not include the removal of live branches.  The different types of pruning for mature trees can be performed in the entire tree or in sections of the tree depending on what needs to be accomplished.

Structural Pruning: Structural pruning either continues young tree pruning or initiates pruning to develop one dominant leader.  Trees with one dominant leader and small, well spaced branches are less likely to suffer mechanical failure, and can more effectively compartmentalize the spread of decay within the tree. Structural pruning selectively favors a single, dominant leader by suppressing competing leaders using reduction cuts.  Reduction cuts shorten stems back to lateral branches at least one-third the diameter of the cut stems.  Reduction cuts may need to be done every few years to encourage more growth in the selected leader, and should be performed on tree species that will become large at maturity to: promote longevity, decrease future maintenance costs, and in order to reduce conditions in the tree that could cause harm to people or property.

Thinning: Thinning reduces the density of live branches, increases light penetration to the interior of the canopy and to the ground below the tree, and increases air movement through the canopy for disease control.  Thinning is also performed for safety reasons.  For example, if performed properly, it can reduce the wind-sail effect or aid in weight reduction pruning.  Proper thinning retains the shape of the canopy and does not remove interior living branches.  Removing interior foliage, or lions-tailing, has adverse effects on a tree and should be avoided.

Thinning should result in an even distribution of branches by removing some of the branches from the edge of the canopy, not from the interior.  This type of pruning should not remove more than about fifteen to twenty percent of live foliage in a mature tree and often five to ten percent is enough.  For young trees, up to twenty-five percent live foliage can be removed without harm.  Thinning is a delicate process that removes small diameter limbs, usually in the one to two inch size.  Once completed, it may be difficult to tell that the tree was pruned and it should have most of its live interior growth.

Appropriate cut Inappropriate cut
Reduction cut Heading cut

Reduction Pruning: In the urban setting, trees often grow larger than the space they can occupy.  Reduction pruning is often used to reduce the size of a tree by decreasing the length of one or more branches.  It is also used for clearances and to reduce risk when a limb has become hazardous.  Reduction pruning reduces size while attempting to maintain a tree’s form.

When performing reduction cuts, limbs are cut back to their point of origin or back to a lateral branch that is large enough to sustain the limb and to assume apical dominance.  A common rule of thumb is the lateral branch should be at least one third the size of the removed portion; we normally like to select lateral branches at least half the size of the removed branch.  Most of the removed branches will be two to six inches in diameter.  Never reduce a landscape tree by topping it!  Topping causes a number of problems such as: decay, numerous sprouts, cracks in limbs, root decline, and bark defects, just to name a few!

Raising or Lifting the Canopy: Low branches are usually not desirable on mature trees in the urban setting.  Low branches can be kept small using reduction cuts until they are removed.  Upright growth from these low, undesirable branches needs to be removed.

Canopy raising, or lifting, is performed on young and middle aged trees to prevent low, non permanent branches from growing to a large diameter.  These branches are valuable to the tree because they help increase overall growth and they improve trunk taper, which increases trunk strength.  Branches below the lowest permanent branch should be removed when they are about half the size of the trunk and after the bark in that area of the trunk has become thick and grooved, or once a branch bark ridge has been established. Regular reduction cuts suppress limb growth while the branch bark ridge forms, until they are later removed.  This simple technique is less damaging for the tree because it prevents having to remove large limbs at the main stem.

cleaning the canopyCrown or Canopy Cleaning: Crown Cleaning includes the removal of dead, diseased, detached, and damaged branches. Crown cleaning is normally performed on middle aged or mature trees for the safety of people and property and to make the tree more attractive.  Crown cleaning can also be used to shorten branches with included bark to reduce the risk of failure and to address limbs with cracks or other structural defects.  A few water sprouts, or “suckers” can be removed but most of the sprouts should remain, removal of all internal sprouts can be very damaging to a mature tree.


III. Pruning Palms

Palms and cycads need regular pruning to keep them attractive and safe.  Many palms maintain a set number of live fronds.  For palms, a regular turnover of foliage occurs as dying lower fronds are replaced by new ones.  Dead fronds are not harmful to the Palm tree but they are a safety hazard, can provide shelter for all kinds of unwanted pests, and can become a fire hazard.  An excessive amount of older yellow fronds could indicate a nutrient deficiency of either: potassium, magnesium, or manganese.  Determine the cause of the problem because pruning or fertilizing with high nitrogen or the wrong type of fertilizer will only worsen this problem.

Before pruning palms, determine the reason you are pruning and the objective you want to accomplish.  Remove dead and dying fronds and developing flowers and fruit.  It is better not to remove live, healthy fronds, however, if you must remove healthy fronds, avoid removing fronds that are growing upward and be careful about removing fronds growing horizontally.  Excessive live frond removal can permanently reduce the set number of fronds a palm maintains.  When removing a frond, sever the frond close to the petiole base.

There is little reason to shave or strip the trunk smooth, although it does no harm to the palm.  The pineapple shape crafted at the base of date palms is not necessary for good health.
Illustrations, PowerPoints or photos by Edward F. Gilman, Professor, Environmental Horticulture Department, IFAS, University of Florida.

Visible Collar No Visible Collar Included Bark

Tree and Shrub Fertilization

“Fertilization is the most cost-efficient maintenance you can do for your trees.  Your trees and shrubs should be on an annual program of slow release fertilization.  A healthy tree, able to cope with city life, adds value to your property and to your quality of life.”

Tree fertilizerAll trees need essential minerals and nutrients to grow and remain vigorous.  In the forest, these nutrients are provided by decomposing leaves and wood.  In our yards we routinely remove this debris, robbing our trees of the essential products they require to produce food. Many tree owners are under the false impression than lawn fertilization will provide their trees adequate nutrition.  Our grass lawns are very efficient competitors and little fertilizer gets past the grass to the trees.  Fertilizing grass and adding and adding a little extra for the trees does not work well.

The root system of an open grown tree spreads out about two to three times the height of the tree, much further than most people would imagine.  Around our homes, we restrict this root spread with barriers such as streets, foundations, underground utilities, and sidewalks.  Essentially, our trees are like potted plants and we need to provide fertilizer much as we would for a house plant. Fortunately, our native trees are able to endure some very challenging conditions.  Some conditions are natural; like the drought we frequently experience.  Others we cause; such as topping, cutting roots, compaction, and chemical burn.  Providing supplemental nutrients to confined root zones helps trees develop better root systems to better cope with these adverse impacts.

Deep root fertilization is the best method for installing fertilizer into the root zone of a tree.  The aeration that occurs in the process helps counter compaction and adds oxygen to the soil.  The water that carries fertilizer into the soil is very beneficial during drought conditions.

We recommend fertilization of your trees and shrubs on an annual programmed plan with a complete organic fertilizer.  In Texas, our recommendation is BioPak PlusBioPak Plus is a blend of beneficial rhizosphere bacteria and water- soluble chelated micronutrients, organic amendments, and yucca plant extract.  Nitrogen fixing bacteria use atmospheric nitrogen that eventually biodegrades into forms used by your tree.  Phosphate-solubilizing bacteria convert the phosphate abundantly available in our soils into soluble forms.

An organic nutrient complex enriches the soil profile immediately surrounding roots, increasing organic content of the soil, and improving nutrient availability.  The micronutrient package has chelated iron, manganese, magnesium, boron, and zinc; all formulated in water soluble forms.  Yucca extract is also present to help with compaction and sulfur to help lower pH.  Sea kelp adds a little nitrogen, and humic acids improve nutrient uptake.

BioPak has a system of microbial activity that through decomposition of natural and introduced organic matter makes essential mineral elements soluble so that they are available to plants for metabolic requirements and normal growth.  BioPak enriches the organic content of the soil profile and helps restore the bioactivity to sterile or depleted soils.  Its microbial activity encourages soil aggregation that over time improves soil porosity, water movement, drainage, and aeration.  This soil fertility program will not burn or harm roots.

In severe cases, complete organic fertilizers can by supplemented to help correct critical problems such a compaction after construction or iron chlorosis.  We sometimes add Mycor to help restore beneficial mycorrhizal fungi to compacted soils after construction.  In central Texas we often add additional chelated iron (138-Fe) to help with iron chlorosis and may even recommend foliar spray in severe cases.  In cases of zinc deficiency, we only recommend foliar sprays because our soils tie up zinc faster than plants can pick it up even when it is chelated.  Most blends of complete fertilizers are not adequate to overcome extreme problems and require some sort of supplement aimed at the specific problem.

Fertilization is the most cost-efficient maintenance you can do for your trees.  Your trees and shrubs should be on an annual program of slow release fertilization.  A healthy tree, able to cope with city life, adds value to your property and to your quality of life.

David Vaughan,
Certified Arborist
Etter Tree Care


Tree Preservation in Construction Areas

Etter Tree Care recommends the following considerations when protecting trees in construction areas.

  • Barricades or fencing should be installed around the trees near drip line before any equipment has access to the property.
  • Pruning, fertilization, and other tree care should be done before construction begins.  Keeping a tree healthy is much easier and less expensive than bringing one out of decline.
  • Mulching protected root zones with wood chips helps reduce compaction.  Mulch should be 4-6 inches deep.
  • The roots are the most important part of the tree.  They extend out 2 to 3 times the height of the tree and almost all of the roots are in the top 12 inches of soil.  Deep rooted trees do not exist in our area.
  • Roots require oxygen to function.  Covering roots with soil, paving or water kills the fine feeder roots and stops their function until roots are able to grow into soil zones with proper oxygen.  Damage is noticeable in the crown 1-3 years later.
  • Grading or removing soil from around a tree removes their absorbing roots with crown damage visible in 1-3 years.  Any cuts or trenches 12 inches deep cut all of the tree roots on that side of the tree.
  • Compaction of soil under trees by heavy equipment or by repeated parking of cars and trucks is as damaging to trees as covering their roots with asphalt or cutting the roots with a trencher.  Even “light” equipment crushes fine roots.
  • Designate specific entrance and exit routes for all traffic.  Do not allow drivers to have unlimited access to the site.  Confining compaction to limited areas helps save trees and makes it easier to correct compaction after construction.
  • Designate specific areas to be used for construction waste, supply storage, and equipment servicing.
  • Do not burn near any tree.  Heat and smoke kill leaves and smaller branches.  Roots extend out 2-3 times the height of the tree.  Do not burn over the root zone of the tree.
  • Diesel vehicles often damage tree branches when they are left running in one spot for extended periods.  No hot tar pots are to be parked under the branches of trees.
  • Oak Wilt is a serious concern and Oak Wilt guidelines must be followed.

Helpful Terms


Apical Dominance – A condition where the terminal bud inhibits the growth and development of lateral buds on the same stem

Branch Bark Ridge – A raised line of bark that forms on the upper side of where the branch joins the trunk

D.B.H. (Diameter at Breast Height) – diameter outside the bark measured at breast height, 4.5 feet or 1.37m

Dominant – A tree branch or leader that exhibits strong apical control, resulting in an upright tree with a strong central leader

Co-Dominant – multiple leaders competing with each other

Included Bark – Bark that becomes embedded in a crotch between branch and trunk or between co-dominant stems, forming a weak union

Lateral Bud – Bud located on the side of a stem

Lion Tailing – Pruning that removes an excessive amount of interior branches, leaving only a few branches at the very end of a limb, displacing foliar weight to the end of branches.

Node – The slightly enlarged portion of a stem where leaves and buds emerge; the joint of a twig

Petiole – The stem of a leaf

Scaffold Branches – The permanent or structural branches of a tree

Terminal Bud – The bud located at the end of a twig or shoot

Wind-sail effect – The movement of air causing a limb to move and bend