Soil is a mixture of mineral particles, organic and inorganic molecules, water, air, and a vast number of organisms. When we realize that a foot of soil sifted from an acre of land will contain up to 3 tons of living organisms, we realize that soil supports a lot of life that we maybe never appreciated.
If much life is supported in soil, then there is no surprise that water must be available. We will study this later in the course, but water is obviously one of the essential materials for virtually all forms of life. The organisms need to exchange gases with the environment, so no surprise that air is a critical component of soil. For aerobic organisms the 22% Oxygen gas (O2) is the critical part of that air. Flooded soils have plenty of water, but the air spaces become filled with water and the soil organisms drown. It is easy to kill plant roots with over-watering! Because all organisms die, then the presence of organic particles in soil is also no surprise.
The water in the soil dissolves organic and inorganic molecules that are also critical for living organisms. These enter the food chain through the roots of plants primarily, so the story of water and minerals begins in the soil.
The mineral particles in soil can be solid bedrock pieces, boulders scraped from bedrock by glaciers, rocks, stones, and even gravel. But these particles are too large to be interacting well with plant roots. Here in New England, USA, the shallowly-buried rocks in our soil allow seedlings of large-tree species to become established over a boulder a half-meter down in the soil. As a tap root cannot penetrate the boulder to grow straight down, it branches out and forms many lateral roots that grow over and around the boulder. The tree may live for many years thereafter, but one year there will be rain and a hurricane that hits New England, and this tree will fall because it never established the woody tap root system that it needed to withstand the forces of that wind in a wet soil.
The mineral particles that matter physiologically to plants are smaller than gravel. They are: Sand, Silt, and Clay as shown in the table below:
As you can easily observe, sand is a great particle for allowing drainage of water (percolation) and for allowing air to enter the soil environment...but it is lousy at holding water and minerals for plants.
Clay is great at holding water and minerals for plants, but has terrible drainage and easily suffocates plant roots.
Silt is not a very good, nor a very bad particle for any of the essential features.
Thus the best kind of soil is a suitable mixture of all three of these sizes of particles. This optimal soil composition is called loam (rhymes with foam everywhere but in New England where it rhymes with loom...strange for a place where textile mills were common in the past).
To determine the soil type (mixture of these three critical particles), one can use precipitation rates to assist. A soil sample is mixed with water containing a surfactant (SURFace ACTive AgeNT). One such chemical is sodium hexametaphosphate, the main ingredient of the laundry water softener, Calgon™. Two tablespoons (not a measurement really) of this powder mixed in a liter of water will do just fine. The surfactant will coat the particles as we shake the soil with the Calgon solution to break up clumps. The coated particles will not re-clump, and will settle out of the slurry based on particle size. If we do our mixing in a glass graduated cylinder this is easily analyzed the next day (clay takes a long time to precipitate).
The bottom layer will consist of sand. The particles are visible and so are the voids between them. The volume of this layer can be determined from the scale on the cylinder. Above the sand layer is a silt layer. The silt particles are visible but the voids are not. The volume of silt can then easily be taken as the difference between the top of this layer and the top of the sand layer. Above the silt layer is a clay layer. The clay particles are too small for our vision and so this layer appears to be completely homogeneous. The difference between the top of this clay layer and the top of the silt layer is the volume of clay. There is, of course, a layer of dirty-looking Calgon solution above the clay layer and some organic particles may be floating on the surface of that.
The volume of each particle layer can be expressed as a percentage of the total volume of soil in the cylinder (NOT INCLUDING THE CALGON!). The sum of these three percentages should total 100%. These percentages can then be used to determine the soil texture type using a soil triangle. An example is shown below:
|Clay 30 mL||Total = 100 mL||30% Clay||Sandy Clay Loam|
(from triangle below)
|Sandy = drainage + air|
|Silt 20 mL||20% Silt||Clay = minerals|
|Sand 50 mL||50% Sand||Loam = good for plants|
Plants and animals cannot complete their life cycle without certain dissolved mineral ions. Such minerals are called essential. Typically essential elements of the periodic chart are part of some critical molecule in the physiology of the organism. These minerals are dissolved from the soil particles of all sizes by the water in the soil. What are these essential mineral elements? The list is divided into two sections: macroelements and microelements. One thing you will notice is that Fe (iron) is found in leaves in proportions similar to S and P, so it is in the macroelements list!
A catalog of the periodic chart of the elements would certainly reveal some as incredibly common in plant structure. So much of each of these is needed in the plant body, that these are called Macroelements. It is critical to note here that when some authors say "nutrient" they are not talking about an energy source at all, or a food of any kind, but rather as an essential mineral that needs to be taken in and used. So "plant food" is not "food" in the human sense (carbon and energy source), but rather as a mineral source. That distinction is important, which is why I stick to the chemistry name, "element." Here are the macroelements:
|source||air & water||limited in soil||usually common in soil|
It is no surprise that carbon, hydrogen, and oxygen are needed in bulk. Carbon forms the skeleton of the organic molecules in the dry-weight of the organism. Hydrogen and Oxygen comprise 90% or more of the weight of a plant, in the form of water. Getting access to these three elements is usally not much of a problem. A few of the rest of the macroelements are difficult to obtain because they are limited in the soil. These are often the important components of fertilizers. Indeed packaging of fertilizer is required by law to have a prominent listing of its "guaranteed analysis." These are three numbers, separated by hyphens, found in large type on the package (example 5-10-15). These numbers indicate the percentage of nitrogen (N), phosphorus (P), and potassium (K), respectively. The example fertilizer is 5% nitrogen, 10% phosphorus, and 15% potassium by weight. The numbers are a bit misleading as, for example, phosphorus is expressed as phosphate which as any chemist knows is as much oxygen as it is phosphorus.
When minerals are deficient, the growth of the plant is stunted or the plant shows other symptoms. The combination of symptoms observed for deficiency of a particular mineral can be traced to the roles that mineral plays in metabolism or physiology. Stunted growth is a symptom for many deficiencies, especially stunted stems with nitrogen deficiency and stunted roots in phosphorus deficiency.
Chlorosis, decreased chlorophyll synthesis or increased chlorophyll degradation, is observed with magnesium, nitrogen, and iron deficiencies. Magnesium is the central atom for the electron cloud of chlorophyll from which electrons flow through the light reactions.
Necrosis, dead spots or zones, is observed when magnesium, potassium or manganese deficiencies are present.
Color changes such as excessive anthocyanin production is observed in stems with phosphorus deficiency. They generally pick up an intense purple color sometimes extending onto the leaves.
Elements are considered mobile if the deficiency symptoms appear mostly in the lower leaves. Obviously the element has moved to the younger parts of the plants. Mobile elements include: nitrogen, phosphorus, magnesium, and chlorine.
Minerals that are considered immobile produce symptoms in the younger leaves instead. The minerals initially sequestered by the plant when it was younger were invested in its leaves which are now the oldest ones on the plant. The mineral is now exhausted in the soil and the younger zones suffer the symptoms because the minerals are held by the older leaves. Immobile minerals include: calcium, boron, and iron.
Many minerals show an intermediate mobility in that the symptoms appear throughout the plant. Minerals of intermediate mobility include: potassium, zinc, copper, manganese, and sulfur.
Some of the roles for the macroelements and their deficiency symptoms are shown in this table:
|P||nucleic acid, phospholipid, reproduction, ATP||stunted, dark leaves, necrotic spots, anthocyanin in stem and leaves, thin weak stem|
|K||ion balance, respiration enzymes||marginal chlorosis, necrosis at tips and edges, curled/crinkled leaves, old leaves first, short weak stems, susceptible to diseases|
|N||amino acids, nucleic acids||stunted, chlorosis of older leaves, abscission, thin stems with lignin or anthocyanin as "sink" for photosynthate|
|S||cysteine, methionine, CoA, etc.||chlorosis of young leaves first|
|Ca||enzyme cofactor, cyclosis, pectins||hooked leaves, necrosis of young meristems, severe stunting as meristems die|
|Fe||cytochromes in resp and psn, enzymes||chlorosis between veins on young leaves first|
|Mg||chlorophyll element, enzyme cofactor||chlorosis between veins on older leaves first, early abscission|
In New England, where acid rain and granite bedrock combine to acidify the soil, we often need to add ground limestone to our upland soils. Plain limestone is Calcium hydroxide and Calcium carbonate and can raise the pH and provide additional calcium (note is a macroelement for plants) that is often leached from our soils already. Dolomitic limestone also contains Magnesium hydroxide and this can provide a boost to our leached Mg ion pools too!
Everywhere you go on earth you will find that subsoils are red. This is because the earth is a ball of iron with a crust of iron oxides and iron sulfides. So iron is almost never a limiting mineral if the pH of the soil is right.
Sulfur is a common element in soils as sulfides are common in the crust. If you have been around the geyser pools, paint pots, and mud pots at Yellowstone National Park or any other volcanic area of our planet, you have smelled the gas emanating from melting rocks below the surface: H2S. This is the "rotten eggs" gas and is good evidence for sulfur as "easily available."
A list of dissolved mineral elements that are found in plants in only trace amounts is shown below. These microelements are just as important to plants as macroelements; the difference is not how critical they are, but in how much quantity is needed. For the plant to survive, it has an absolute requirement for just a trace of certain elements. Most of these are enzyme cofactors of various sorts (see table below). Fortunately only a trace of each one is required, so that most soils have sufficient quantities of these for plant growth. Generally most places in the US do not need to add microelements to the fertilizers used. For New England, this is not particularly true however. Our acid rain has leached these microelements out of our soils and so it is wise for New England farmers to use fertilizers that include microelement supplements.
|Mn||1||resp/photolysis enzyme cofactor||chlorosis and small necrotic spots throughout plant|
|Cu||0.1||enzymes, plastocyanin, cytochrome oxidase||dark green leaves with necrotic spots at tips of young leaves, early abscission|
|Zn||0.3||enzyme cofactor, chlorophyll synthesis, IAA synthesis||decrease internode length (rosette look), puckered leaf margins, chlorosis of older leaves with white necrotic spots|
|Si||(30)||cell wall rigidity in Equisetum and grasses||soft stems that lodge (fall over)|
|Mo||0.001||nitrate reductase cofactor||enzyme converts nitrate into nitrite so symptoms are like N deficiency|
|B||2||pollen tube growth and orientation, nucleic acid synthesis, membrane synthesis||black necrosis at base of young leaves and buds, stiff/brittle stems, meristem death followed by excessive branching|
|Al||enzyme cofactor||difficult to have too little-toxicity more likely|
|Cl||3||ion balance, photolysis, cell division||wilting leaf tips, bronze leaves, rare to be deficient in field|
|Na||0.4||C-4 regeneration of PEP step||chlorosis, necrosis, flowering failure in C-4 plants only|
|Ni||0.002||urease cofactor||urea accumulates in leaf tips causing necrosis, unlikely in field|
The following graph demonstrates how deficiency of any macroelement or microelement reduces growth. As the mineral availability is increased, growth increases. As the mineral content continues to be increased there is not much further increase in growth, but other qualities of the plant may be continuing to increase. This zone is called the luxury consumption zone. However, continuing to increase the mineral concentration ultimately reaches toxic levels and growth is diminished.
The goal of a plant grower is to keep the plant in the "sufficient" to "luxury" zone but never to get as low as deficiency nor as high as toxicity for any one of the macroelements or microelements. The trouble with that goal is knowing how wide the luxury zone is in terms of concentrations. For minerals like boron, the zone is very narrow and it is easy to achieve toxic levels or to be in deficiency. For minerals like phosphorus, the luxury zone is quite broad and large amounts can be given and the plants will respond nicely in spite of that. As a result it is difficult to overdose plants on phosphorus.
We will discuss water in detail later in the course, but for now the main concept that needs to be mentioned about it is that water dissociates:
H2O ↔ OH- + H+
The concentration of dissociated water in freshly-distilled water is 10-7 M. Scientists developed an easy way to describe the amount of dissociated H+ in a solution. This description was called the pouvoir Hydrogéne which we know today as pH.
pH = - log [H+] = - log [10-7M] = 7 for fresh distilled water
When distilled water is left in contact with the atmosphere for awhile, it absorbs carbon dioxide from the atmosphere:
CO2 + H2O ↔ H+ + HCO3- ↔ H2CO3
In this way, "old" distilled water has a pH of about 5.6. The pH of this water can be restored to pH 7 by heating the water. This evaporates the carbon dioxide back into the atmosphere, driving the equilibrium to the left, restoring neutral pH.
The pH scale runs from 0 to 14 and some examples and so on are shown below:
|H+ Conc:||100||10-7||10-14 M|
|Optimal for plants:||cranberries||common|
The original European settlers tasted the soil to measure its pH. Alkaline soils were mapped out to avoid that unpleasantness so you will see geographic features such as: Bitter Creek, Bitter Valley, Bitter Run, and so on. Neutral soils were called "sweet" by the settlers. For sour soils like those here in New England, the settlers found limestone to raise the pH. Old farmers still refer to liming a field as "sweetening" the soil. Limestone is used on athletic fields on campus for yardlines and other field markers. The grass in the turf grows better where these markers are because of the pH control and the improved concentrations of Ca and Mg in the local soil.
Ca(OH)2 + 2 H+ ↔ Ca+2 + 2 H2O
If you bought an acre out in Bitter Canyon out west, limestone would not be what you seek to lower the pH in your alkaline soil. You would need to use aluminum sulfate to acidify it:
Al2(SO4)3 + 6 OH- ↔ 2 Al+ + 3 H2SO4 + 3 O2
The relationship between soil pH and mineral availability is shown below:
A clay particle (much enlarged here) is covered with negative charges:
Opposites attract, so metal ions with positive charge(s) stick all over the surface of the clay particle:
It is not too surprising, now, why clay is so good at holding minerals compared to silt or sand. The clay particles are the smallest of the three mentioned above, so a cubic meter of clay would have a vast amount of surface area...all coated with negative charges. This would present a wonderful way to grab onto those mineral ions and hold them. One of the main odor constituents of urine is ammonium ion which carries a positive charge. It is no surprise that clay is the main constituent of cat litter for litter boxes.
The root hair cells of plant roots secrete H+ into the water around nearby clay particles. These smaller H cations replace the larger macro- and micro-element cations:
The released cations are now available for uptake into roots. The plant takes those in through the endodermis of the root by special transport proteins in the cell membrane of endodermal cells.
Of course, if it is raining acids (H+) as it does in New England, the minerals are all released en masse and can leach out of the soil before the roots can get them. The soil is left stripped of minerals. It is little wonder that the poor soils of New England cannot compete with the productivity of mid-western soils that have extensive pH buffering and no complications of acid rain!
For some minerals, the soil pH determines how they react in the chemistry of the soil. Iron, zinc, manganese, copper, and calcium at the wrong pH can become deficient by means of precipitation as an insoluble form unavailable to plants. Iron is perhaps the most-famous case:
|2 Fe3+ + 6 OH-||alkaline pH|
|2 FeOH3 --> Fe2O3. 3H2O = insoluble rust|
The precipitation deficiency can be ameliorated by the use of chelating agents (ligands) place in the soil water. These compounds interact with the metallic ions to shield them from the precipitation reactions. Electrons from -COOH or -NH4+ groups on these chelating agents prevent the oxidation reactions.
Synthetic chelating agents used to deliver minerals include EDTA and EDDHA. EDTA is Ac2N-CH2-CH2-NAc2. This is known as Ethylene Diamine TetraAcetic acid; the commercial product is called Versene™. EDDHA is Ethylene Diamine Di (o-Hydroxyphenyl) Acetic acid; the commercial product is called Sequestrene™
The way these chelators work to shield a mineral ion is shown below.
Before one should use such a chelating agent, it would be wise to find out if the chelator also shields the ion from uptake by the plant. In general, dicots can overcome chelators and remove the necessary ion. Grasses, such as corn are less able to do so.
Natural chelating agents include: catechols (remember, the substrate for the polyphenol oxidase reaction?) produced by soil bacteria, hydroxamates (peptides) produced by soil fungi, and citrate produced by plant roots. These soil chemicals assist in keeping minerals available to plant roots.
Because soil is a mixture of many particles, differing with source, and also organisms of many species, the soil can often present a problem of controls for experiments, and side effects of bacterial or fungal interference. For this reason, plant physiology experiments often need to eliminate soil.
Culturing plants in containers without soil is called hydroponics. This has been a popular diversion for those who like to grow plants since 1938 when Hoagland came up with a suitable mix of minerals and chelating agents. In laboratory we initiate a mineral nutrition project. Using the recipe that you find in your lab handout, you will prepare a table like that below for your abstract amplification material: