31.0: Prelude to Soil and Plant Nutrition - Biology

31.0: Prelude to Soil and Plant Nutrition - Biology

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Cucurbitaceae is a family of plants first cultivated in Mesoamerica, although several species are native to North America. The family includes many edible species, such as squash and pumpkin, as well as inedible gourds. In order to grow and develop into mature, fruit-bearing plants, many requirements must be met and events must be coordinated. Seeds must germinate under the right conditions in the soil; therefore, temperature, moisture, and soil quality are important factors that play a role in germination and seedling development. Soil quality and climate are significant to plant distribution and growth. The young seedling will eventually grow into a mature plant, and the roots will absorb nutrients and water from the soil. At the same time, the aboveground parts of the plant will absorb carbon dioxide from the atmosphere and use energy from sunlight to produce organic compounds through photosynthesis. This chapter will explore the complex dynamics between plants and soils, and the adaptations that plants have evolved to make better use of nutritional resources.

31.0: Prelude to Soil and Plant Nutrition - Biology

An International Journal on Plant-Soil Relationships

Plant and Soil publishes original papers and review articles exploring the interface of plant biology and soil sciences, and that enhance our mechanistic understanding of plant-soil interactions. This includes both fundamental and applied aspects of mineral nutrition, plant-water relations, symbiotic and pathogenic plant-microbe interactions, root anatomy and morphology, soil biology, ecology, agrochemistry and agrophysics. Articles discussing a major molecular or mathematical component also fall within the scope of the journal. All contributions appear in the English language.

The Editor-in-Chief is Hans Lambers, University of Western Australia, Crawley, Australia.

Why publish with us

  • We explore the interface of plant biology and soil sciences .
  • We provide high levels of author satisfaction , with 96% of our published authors reporting that they would definitely or probably publish with us again .
  • Through Springer Compact agreements , authors from participating institutions can publish Open Choice at no cost to the authors .

III. The Soil Profile

Most naturally occurring, undisturbed soils have three distinct layers of variable thicknesses. The layers are the topsoil, subsoil, and parent material. Each layer can have two or more sublayers called horizons. Collectively, the horizons make up the soil profile. The predominate parent material varies by location in North Carolina. In the NC piedmont and mountains, the parent material is typically weathered bedrock known as saprolite. In the river bottoms and stream terraces of the NC piedmont and mountains, the parent materials are the floodplain sediments delivered from upstream where erosion has occurred. In the NC coastal plain, the parent materials are marine sediments deposited over eons as the oceans go through the natural cycles of advance and retreat. In the easternmost NC coastal plain, the dominant parent material is organic matter. These organic soils are typically found in areas that just 50,000 years ago were below sea level. Such areas are swamps where plants grow and thrive. But these areas are too wet for the plant residues (leaves, branches, roots, trunks, and the like) to efficiently decompose.

Soils&rsquo properties vary with the soil depth. The surface soil, or topsoil layer (O and A horizon in Figure 1&ndash2), usually contains less clay, but more organic matter and air, than the lower soil layers. Topsoil is usually more fertile than the other layers and has the greatest concentration of plant roots.

The subsurface layer (B and C horizon in Figure 1&ndash2), known as subsoil, usually has a higher clay content and lower organic matter content than the topsoil.

Soil properties often limit the depth to which plant roots can penetrate. For example, roots will not grow through an impenetrable layer. That layer may be bedrock (Figure 1&ndash3), compacted soil, or a chemical barrier, such as an acidic (very low) pH. A high water table can also restrict root growth due to poor soil aeration. Few big trees grow in shallow soils because big trees are unable to develop a root system strong enough to prevent them from toppling over. Shallow soils also tend to be more drought-prone because they hold less water and thus dry out faster than deeper soils. Water lost to runoff on shallow soils would instead be absorbed by a deeper soil. In addition, deep soils allow the roots to explore a greater volume, which means the roots can retain more water and plant nutrients.

Soils change in three dimensions. The first dimension is from the top to the bottom of the soil profile. The other two dimensions are north to south and east to west. The practical meaning of this three-dimensional variability is that as you move across a state, a county, or even a field, the soils change. Five factors of soil formation account for this variation:

  1. Parent material
  2. Biological activity
  3. Climate
  4. Topography
  5. Time

Differences in even one of these factors will result in a different soil type. Soils forming from different parent materials differ. Soils forming from the same parent material in varying climates differ. Soils at the top of a hill differ from soils at the bottom. The top of the hill loses material due to natural erosion the bottom gains the material from above. Considering the number of possible combinations of these five factors, it is not surprising that more than 450 unique soil series are currently mapped in North Carolina. Globally, more than 20,000 different soil series occur. Neighborhood level soil series can be found by typing &ldquoWeb Soil Survey&rdquo into any Internet search engine.

John A. Kelley, USDA-Natural Resources Conservation Service

Figure 1–2. Soil horizons.

John A. Kelley, USDA-Natural Resources Conservation Service

Figure 1–3. The Craggey soil series an example of shallow soil.

John A. Kelley, USDA-Natural Resources Conservation Service

Figure 1–3. The Craggey soil series an example of shallow soil.

John A. Kelley, USDA-Natural Resources Conservation Service

Mycorrhizal Symbiosis

The roots of most plants are colonized by symbiotic fungi to form mycorrhiza, which play a critical role in the capture of nutrients from the soil and therefore in plant nutrition. Mycorrhizal Symbiosis is recognized as the definitive work in this area. Since the last edition was published there have been major advances in the field, particularly in the area of molecular biology, and the new edition has been fully revised and updated to incorporate these exciting new developments.

The roots of most plants are colonized by symbiotic fungi to form mycorrhiza, which play a critical role in the capture of nutrients from the soil and therefore in plant nutrition. Mycorrhizal Symbiosis is recognized as the definitive work in this area. Since the last edition was published there have been major advances in the field, particularly in the area of molecular biology, and the new edition has been fully revised and updated to incorporate these exciting new developments.


Plant nutrition is a field that crosses borders and that touches corners of several disciplines in the area of the nutritional sciences. On the one hand, plants require a multitude of essential and non-essential nutrients for proper sustenance and development. The uptake, transport, and accumulation of these micro- and macronutrients must be tightly regulated in order to avoid both deficiency and toxicity, and to regulate the plant's nutritional status to maintain an ideal equilibrium. On the other hand, fiber, protein, non-saturated fats, and phytochemicals (e.g. carotenoids, folic acid, alkaloids, polyphenols), besides having demonstrable critical functions in plant metabolism, have also gained visibility within human nutrition due to their health-related benefits. In fact, a safe and sufficient plant food supply is essential for humanity, since directly or indirectly, plant foods constitute our most important source of dietary nutrients.
In this context, section Plant Nutrition will consider submissions that deal with aspects of plant nutrition from both a plant standpoint (e.g. studies aimed at understanding diverse processes of nutrient uptake, transport, metabolism, and storage) and a human perspective (e.g. strategies to modulate nutritional and anti-nutritional content of plant foods bioavailability of plant nutrients in the human gut novel plant food sources with high nutritional content validation of bioactivity of phytonutrients for human health). As such, we welcome papers that cover the entire scope of plant nutrition, bringing forward an integrated forum addressing the activities and functions of micro- and macronutrients needed for plant growth, but also showcasing the important role of plant foods in nutrient delivery for optimal human and animal health.

Please consider the requirements for experimental studies as listed below

Studies using transgenic or mutant plants should be based on data from multiple independent alleles (at least 2) displaying a common and stable phenotype. Examples include, T-DNA, transposon, RNAi, CRISPR/Cas9, chemically induced, overexpressors, reporter fusions (GUS, FPs, LUC) etc. Qualitative data can be presented from a single allele but should be indicative of observations from multiple alleles which should be explicitly stated in the text. Quantitative data should be derived from multiple alleles (at least 2) and should be displayed separately for each allele (with at least 3 independent replications for each allele). Studies reporting single alleles may be considered acceptable when:

i) Complementation via transformation is used for confirmation
ii) The allele has been previously characterized and published and is representative of multiple independent lines
iii) Systems where genetic transformation is difficult or not yet possible, alternative evidence should be presented supporting the reported allele.


Sugarcane (Saccharum spp.) farming systems globally have largely transitioned away from burning the crop prior to harvest. Harvesting the sugarcane crop ‘green’ results in large volumes of biomass residues being left on the soil. Despite this, there is little evidence for increased soil organic carbon stocks. We investigated the role of surface application or incorporation (0–200 mm soil layer) of harvest residues (15 t dry weight residues ha −1 ) and its biochar (5.4 t ha −1 based on the quantity of resource recovered after pyrolysis) on the priming of native soil organic carbon (SOC), the mineralisation of the organic amendments and the source of crop nitrogen (N) uptake (soil, organic amendment or urea). All treatments received urea at 180 kg N ha −1 . To achieve the separation of C and N sources, dual 13 C and 15 N-enriched sugarcane residues and corresponding biochar (350 °C) were used in an 84-d controlled environment study. A three-pool isotope mixing model, utilising two levels of 13 C enrichment in residue (16.6‰ and 23.8‰) and biochar (16.8‰ and 24.1‰), was also applied to partition the C from three sources: 1) root respiration, 2) organic amendment mineralisation, and 3) SOC priming. The SOC mineralisation was increased following both surface-applied and incorporated residues, over the nil organic amendment (control) by 72.3 and 78.3 CO2–C m −2 respectively over 84 days. In contrast, biochar lowered the mineralisation of SOC by 62.9 g CO2–C m −2 compared to the control. The cumulative mineralisation of sugarcane residue biochar (18.9 g CO2–C m −2 ) was lower (P = 0.03) than surface applied residue (50.1 g CO2–C m −2 ) and incorporated residue (71.9 g CO2–C m −2 ) over the study period. While there were no differences in total crop N uptake between the organic-amended soils and the control, the source of N was significantly different. The sugarcane plants utilised 31.0% and 29.4% of the supplied urea N in the nil organic-amended control and biochar treatment, respectively. This was significantly reduced to 24.8% and 20.6% in the surface residue and incorporated residue treatments, respectively. In comparison, the plant uptake of N derived from the organic amendments was 27.8%, 15.4% and 6.4% from incorporated residues, surface-applied residues and biochar, respectively (P < 0.001). Results suggest that the increased mineralisation of SOC, partly driven by the high C:N ratio (73:1) and the unbalanced nutrient stoichiometry may lead to low SOC accumulation from surface residue application and that sugarcane residue biochar results in SOC stabilisation and an increase in the use efficiency of fertiliser N in sugarcane systems.

Ground Force’s High Calcium Pelletized Lime provides high levels of calcium to the soil in order to combat acidity within the soil. At Ground Force, we pulverize our mined limestone into a fine powder before pelletizing it to allow for rapid release upon usage.

  • Calcium (Ca): 33%
  • Calcium Carbonate Equivalent: 86%
  • Water Soluble Binder-lignosulfonate: 2%
  • Moisture (Maximum): 1%
  • Our pelletizing procedure grants an even spread of our product to ensure that calcium is placed evenly through the soil. Calcium is an essential component in the plant cell wall, and needs to be present in order for new cells to grow.
  • Helps increase the pH in acidic soil (soil with a pH below 7).
  • Can help eliminate Aluminum Toxicity.
  • Helps increase the efficiency of other major nutrients like Nitrogen, Phosphorus, and Potassium that plants need.
  • Helps plants to absorb Nitrogen and synthesize proteins.
  • Improves microbial action to help break down pesticides and organic matter.

This signature series can be found in a store near you! List of stores coming soon.

Ground Force’s Gypsum is an excellent source of calcium and sulfur for plants and soil alike. Using pelletized gypsum helps improve soil structure, allows for increases in oxygen and water penetration, removes residual salt from effluent water and repairs salt damage caused by winter de-icing and pets.

  • Calcium (Ca): 21%
  • Sulfur (S): 14%
  • Calcium Sulfate (CaSo4): 68%
  • Water Soluble Binder-lignosulfonate: 2%
  • Moisture (Maximum): 1%
  • Our pelletizing procedure grants an even spread of our product to ensure that both calcium and sulfur are delivered to the soil.
  • Improves the soil structure and compaction of clay soils, which in turn improves the water and oxygen penetration.
  • Stimulates microorganism growth.
  • Helps alleviate blossom end rot.

This signature series can be found in a store near you! List of stores coming soon.

When plants need both calcium and magnesium, Ground Force’s Dolomitic Lime is a great way to get these important nutrients right where they are needed. Dolomitic Lime is a natural source for both of these minerals, and not found in most fertilizers. Magnesium plays a key role in the photosynthesis process of plants and is vital in the overall systems of plant growth. Calcium helps build and strengthen the plant’s cell walls.

  • Calcium (Ca): 17.5%
  • Magnesium (Mg): 10.1%
  • Calcium Carbonate Equivalent: 80%
  • Calcium Oxide (CaO): 17%
  • Magnesium Oxide (MgO): 17%
  • Water Soluble Binder-lignosulfonate: 2%
  • Moisture (Maximum): 1%
  • Our pelletizing procedure grants an even spread of our product to ensure that both magnesium and calcium are distributed evenly throughout the soil.
  • Helps with the photosynthesis process in plants.
  • Supplies Magnesium to acidic soil.
  • Improves the microbial action to help break down pesticides and organic matter.

This signature series can be found in a store near you! List of stores coming soon.

JARS v55n3 - Osmosis and Plant Nutrition

Osmosis and Plant Nutrition
Michael Hammer
Sassafras, Victoria, Australia

Reprinted from the The Rhododendron, Vol. 40, 2000, the journal of the Australian Rhododendron Society.

What is Osmosis?
Imagine we take a container and fill it with water. The water consists of many tiny molecules in constant movement. As these molecules move around they collide with the walls of the container and bounce back, millions upon millions of collisions per second. Each collision exerts a tiny push on the wall and the overall result of all these collisions is a net force on the walls of the container which we call "pressure." The pressure is simply a measure of the number of collisions per square metre per second.

Next, imagine we put a barrier down the middle of the container (see Figure 1) so that there is water on both sides of it. Further, we make this barrier out of a material which has tiny holes in it. These holes are far too small to see, but they are large enough to allow a water molecule to fit through. The water molecules will collide with this barrier just as they collide with all the other wall surfaces. Most of the time they hit a solid part of the barrier and bounce back, but occasionally they will strike the barrier where there is a hole and pass through it. Thus, referring to Figure 1, some water molecules from side A will end up moving into side B and vice versa.

Figure 1. Barrier with water on both sides.

Now imagine we dissolve some salt into side A of our container. Salt molecules are larger than water molecules, and if the holes in our barrier are of the right size they can be big enough for the water molecules to pass through but too small to allow the salt molecules through. Since the pressure on both sides of the barrier is the same, the total number of collisions per second on both sides of the barrier will be the same, but, on side B, all collisions are due to water molecules (which can fit through the holes), whereas on side A some are due to salt molecules (which cannot fit through the holes). Fewer water molecules strike the barrier per second on side A than on side B and thus fewer water molecules will pass through the barrier from side A to B than from B to A. There is a net movement of water from the side of low salt concentration to the side of high salt concentration.

This effect is called "osmosis," and the sort of barrier we've just talked about, with holes large enough for some molecules and too small for other molecules, is called a "semi-permeable membrane." Of course we do not have to use salt any substance which dissolves and has large molecules will cause the same effect.

Osmotic Pressure
The flow of water from one side of the membrane to the other occurs simply because there are more collisions per second of water on one side of the membrane than on the other. The flow will continue until the number of collisions per second of water molecules becomes the same on both sides of the membrane. This can occur in two ways.

Firstly, it can occur if the migration of water causes the concentration of dissolved solids to equalize on both sides of the membrane. This could occur if there was material dissolved in the liquid on both sides of the membrane but at different concentrations.

Secondly, it can occur if the migration of water raises the physical pressure on the more concentrated side of the membrane. More pressure means more collisions per second, and if the pressure is raised enough, the number of collisions due to the water component will balance. This forms a convenient way to measure the osmotic strength of a solution and leads to the expression "osmotic pressure" as a measure of the osmotic strength of a particular solution.

Imagine we have a semi-permeable membrane in the form of a closed sack with an aqueous solution of salts inside it. If we place this sack in a solution with more dissolved solids (greater osmotic pressure), water will be drawn out of the sack and it will start to collapse. If we place the sack in a solution with less dissolved solids (lower osmotic pressure) water will flow into the sack and it will start to swell.

So why is all this relevant to us as gardeners? Well, it turns out that many membranes in nature are semi-permeable. In particular, cell walls are semi-permeable membranes. We may not realize it but we are constantly experiencing the effects of osmosis in everyday life. Here are some everyday examples.

Some Examples of Osmosis
You cut yourself, put seawater on it and it hurts. The osmotic pressure of seawater is much higher than the inside of your cells (seawater is about 2-3% salt) the exposed cells start to lose water and collapse. Put fresh water on it and it also hurts the osmotic pressure of the fresh water is too low, and the cells gain water and start to swell. If you bathe the cut in water with 0.9% salt (saline), however, it doesn't hurt at all: the osmotic pressure of the saline is just right. Try it next time you want to wash a cut or graze. Add 9 grams of salt (about 2 level teaspoons or 1 heaped teaspoon) to a litre of boiled water. You should find that it is much less painful. Of course, be careful - don't add too much salt or the osmotic pressure will become too high and it will hurt again.

In the past people used to salt meat to keep it from spoiling. Why? The bacteria that attack meat do not have an impermeable skin they have cell membranes that are semi-permeable. The osmotic pressure of the salt is so high it sucks the water out of the bacteria cells and kills them. By the way, that is the basis for the belief that bathing a wound in seawater helped to fight infection.

Salt is not the only chemical that raises osmotic pressure. Any soluble molecule large enough to be blocked by the holes in the membrane has a similar effect. One very important class of molecule with a similar effect are the sugars. Bacteria use sugar for food just as we do. Despite this, a strong enough sugar solution will raise the osmotic pressure high enough to kill bacteria and thus prevent spoilage - that's why jams and honey keep well without refrigeration. If you don't believe me, try diluting honey with some water and leave it out for a few days. Compare its lasting qualities with undiluted honey.

The membranes of plant cells are also semi-permeable. There are some simple experiments you can do to show this. Put some raw cucumber slices in a bowl of fresh water and others in a bowl with saturated salt water. The slices in fresh water swell up and become very turgid. The ones in salt water collapse and become completely limp.

Take a half a raw potato, scoop a recess in the cut face and put in a spoonful of salt or sugar. Leave it for an hour or so and you will find the recess filled with liquid, while the potato around the liquid has gone soft and spongy. Some of the salt or sugar dissolves in the little bit of water around the cut face and the high osmotic pressure of this solution draws out more water from the potato cells. Try it with a cooked potato and nothing happens. Why? Cooking destroys the cell membranes so that osmosis can no longer occur.

Effect of Osmosis on Plants' Collection of Water
Root hairs on plants, like other cells, are also semi-permeable. Water gets through readily but dissolved nutrients cannot. Plants, in fact, rely on an osmotic pressure gradient in order to collect water. The concentration of dissolved solids, and thus the osmotic pressure, rises continuously from the soil around the roots to the central water conducting core of the root (called the xylem) and this causes water to flow into the plant. Remember we said osmosis can result in a physical pressure difference across the membrane - this means that the physical pressure is higher in the core of the root than in the soil around the plant. On cool mornings especially, when the soil is damp, you can sometimes see drops of water all round the edges of the leaves on some plants. This arises because the osmotic pressure gradient has forced so much water into the plant it flows out through the ends of the veins at the edges of the leaves and collects as droplets. Botanists call this process "guttation."

By the way, as an aside, did you know that plants cool themselves by evaporating water the same way we do when we perspire? This partly explains why plants burn much more easily when they dry out. Without enough water to evaporate they can't cool themselves adequately and the leaves overheat and die.

The primary molecule raising the osmotic pressure inside plant roots is sugar - manufactured in the leaves and transported down in the phloem tissue to the roots. Plants to some degree can control the osmotic pressure inside their roots. This is done by converting sugar to starch or vice versa. Starch is only sparingly soluble, so it does not contribute much to osmotic pressure. If a plant wants to reduce its osmotic pressure it converts some sugar to starch. To raise the osmotic pressure it can convert some starch back into sugar.

Root hairs do not just collect water for the plant they also collect nutrients by a separate process called "active transport." For this process to work, however, the nutrients have to be dissolved in water. Nutrients in an insoluble form cannot be absorbed by the plant. For example, you can't address an iron deficiency for an azalea by putting some iron filings around the plant. The iron may be there, but it is not in soluble form, so the plant can't take it up. And herein lies a paradox, exactly the same as for the bacteria in honey. Because the nutrients are soluble in water they also raise the osmotic pressure outside the root hairs. A higher nutrient level means more food but it also makes it harder for the plant to collect water. If the nutrient concentration becomes too high the osmotic pressure outside the roots becomes greater than inside the roots. When that happens the flow of liquid reverses. Instead of the plant taking up water and nutrients it can't take up anything. Instead it starts to lose water into the surrounding soil. The plant dehydrates, the leaves are starved of water, they dry out, die and go brown around the edges. We say the plant is being burnt. If the situation lasts too long the plant dies.

Controlling Osmotic Pressure Around Plant Roots
How can the osmotic pressure get to be higher in the soil than in the plant? Firstly and most obviously, you put too much fertilizer around a plant. Less obviously, you fertilize a plant when the soil is very wet, the fertilizer is well diluted and at a reasonable concentration for the plant. Then along comes a dry spell and the soil around the plant starts to dry out. Water is lost but the nutrients cannot evaporate they stay in the soil and the concentration rises and rises. Eventually it gets so high the osmotic pressure reverses and goodbye plant. Another problem is especially relevant to pot plants. Every time you fertilize you add more nutrients to the pot. Normally you add far more nutrients than the plant can actually use. The excess cannot escape and builds up around the plant roots. Eventually the level reaches toxic levels, and as mentioned already this is exacerbated when the mix in the soil dries out a bit. To avoid this, one is told to periodically deep soak pot plants to wash out the excess nutrients.

But another issue needs to be considered as well. What is the osmotic pressure inside the plant? If this is high enough the plant can cope with a higher concentration of nutrients in the soil. Remember sugar was the main molecule raising osmotic pressure inside plants. The osmotic pressure is likely to be highest when there is a lot of sugar around and this occurs when the plant is producing the greatest amount of sugar - and when is that? When it is most active, when it is growing most rapidly. Conversely, the sugar level is likely to be lowest when the plant is dormant. Hence the advice to fertilize plants when they are growing rapidly and the caution to not fertilize when the plant is dormant.

What about cuttings? The greatest problem for a cutting is loss of water. Further, the cutting is using up food reserves to produce new roots. Sugar levels are likely to be pretty low and this means the osmotic pressure inside the plant will also be low. A bad combination. The last thing a cutting in that position can cope with is high osmotic pressure outside the fledgling roots. We want to make the osmotic pressure outside the cutting as low as possible. Fertilizer for a cutting is like poison. It is not that the cutting can't use the nutrients. That is irrelevant it would only mean the fertilizer was wasted. The problem is that the nutrients raise the osmotic pressure and dehydrate the cutting. In fact we probably should be thoroughly washing our mix to remove every trace of dissolved solids to get the osmotic pressure as low as we possibly can.

Regulating the Nutrient Level Around Plants
One of the challenges for us as gardeners is to regulate the nutrient level around our plants. Plants can cope with considerable variation in the level of nutrients around the roots, but they do better if the level is more stable. That's why the comment is made that it is better to fertilize more often with very weak fertilizer than it is to use stronger fertilizer occasionally.

Let's look a bit at ways in which nutrient levels can be stabilized around plants. The key here is that nutrients are available to plants and affect the osmotic pressure only if they are in solution. Nutrients not in solution are completely inert as far as the plant is concerned. You know, what would be really nice would be to have some mechanism which stored nutrients in the soil in an insoluble form and slowly converted them to a soluble form at a rate which keeps a constant level around the plant. You often hear comments that organic fertilizers - compost, manures, etc. - are far better than chemical fertilizers. Environmentalists and "greenies" often wax so lyrical it seems as though the nutrients from organic fertilizers are good and healthy while the nutrients in chemical fertilizers are evil and poisonous. That of course is utter rubbish a potassium ion is a potassium ion whatever the source. Organic fertilizers do, however, have a major advantage. The nutrients in chemical fertilizers are in a readily soluble form. Very shortly after the fertilizer is applied to the soil, the nutrients dissolve, raising the nutrient level and osmotic pressure. The nutrients in organic fertilizers, however, are often locked up in complex organic compounds and do not dissolve readily. When they are applied to the soil it requires the action of microbes in the soil to break down these organic compounds and thereby release the nutrients to dissolve in the soil water. Thus organic fertilizers provide a slow steady nutrient release. In more recent years, inorganic fertilizers have become available which can at least partly match this action. Fertilizer granules are coated with a polymer which prevents the fertilizer dissolving all at once. Instead the nutrient material slowly leaches through the polymer barrier. Depending on the thickness and composition of this barrier, the leaching process can take three, six or nine months. Several proprietary brands are available, of which the best known is probably Osmocote (the name probably comes from a contraction of "osmotic coating").

There is another advantage of organic fertilizers. They leave a residue of partly decayed organic matter in the soil called "humus." This humus changes the way in which soil particles stick together, and also has the property of binding and trapping both water and nutrients. Nutrients can continuously attach and de-attach themselves to humus particles (called an "equilibrium reaction"). When the nutrient concentration in the soil is high, the rate of attachment exceeds the rate of separation. The net effect is that some of the nutrients bind to humus particles and are effectively removed from solution. When the dissolved nutrient level falls, the equilibrium swings the other way and the attached particles go back into solution. In short, the humus acts to stabilize the dissolved nutrient level in the soil water - exactly what we discussed just before. Chemists call this process "buffering." Thus organic fertilizers provide a buffered source of nutrients whereas chemical fertilizers are an unbuffered source.

Humus is not the only thing which can do this. Clay particles such as felspars, silicates, etc., are chemically active materials. Nutrients can adhere and detach from them, just as happens with humus. Again, when nutrient levels are high, attachment predominates and the nutrients are removed from solution but still bound in the soil so that they are not washed away. When dissolved levels fall again the bound nutrients detach, raising the dissolved levels again. By contrast, sand is silicon dioxide which is chemically inert. Nutrients cannot attach to sand particles. As a result, the nutrient level fluctuates much more in sandy soils than in clay and nutrients are much more easily washed away and lost. Clay soils may have problems with poor aeration, compaction and water logging but they are generally more fertile than sands.

Nutrient Availability Versus pH
Osmosis explains how plants absorb water from the soil but it does not account for the way in which a plant collects nutrients. In general, collection of nutrients is a more complex active process (a pumping process which requires the plant to expend energy). It is also a process that varies very greatly from one type of plant to another. In general, if a plant species is growing in an environment where a particular nutrient is very scarce it evolves very efficient ways of collecting that nutrient. Conversely, if the plant grows in an environment where a particular nutrient is very plentiful the collection efficiency for that nutrient can be expected to be very low. Indeed, if the nutrient is normally present in excessive amounts the plant may even develop mechanisms to reject that particular nutrient. A simple example of that is when plants colonize the tidal margins such as saltwater mangroves. In these locations the sodium concentrations (at least) are much higher than the plant can possibly use and these plants need to develop mechanisms to selectively excrete the excess sodium.

If a plant has developed in a region where a particular nutrient is very low and is suddenly placed in an environment where there is a large amount of the nutrient, its super-efficient collection mechanism means that it will collect far too much of the nutrient - possibly a toxic level. Such a plant has no means of getting rid of the excess, because it evolved in an environment where such a mechanism was not necessary. This is, for example, the situation for many Australian natives with regard to phosphorous. This does not mean that Australian natives use less phosphorous for growth. It only means they are more efficient at collecting it and therefore require lower levels of this element in the soil.

Conversely, if a plant species evolved in a region where a nutrient was very plentiful, and it is placed in a new environment where that nutrient is much less plentiful, then the plant may suffer a deficiency simply because it has not developed efficient mechanisms for collecting that nutrient. A good example of that is the Rhododendron genus with respect to iron. Rhododendrons are so inefficient at collecting iron they can suffer chlorosis at available iron levels which would be more than adequate for, say, vegetables.

Remember, a nutrient is only available if it is in solution. It is quite possible for plenty of the nutrient to be present yet not in solution - it may be present as an insoluble salt. A major factor influencing this is the pH of the soil. You can easily show this with a simple experiment. Put some ferrous sulphate (sulphate of iron) in water and shake it up. The ferrous sulphate dissolves to form a clear green solution. Now add some washing soda (sodium carbonate) or some caustic soda (sodium hydroxide) and shake again either of these materials will make the water alkaline. Immediately a dirty brown precipitate forms and the green colour disappears. That brown precipitate contains the iron converted to an insoluble form, a form which is useless to plants. That is why adding ferrous sulphate to alkaline soil makes very little difference to rhododendrons, as the ferrous sulphate is immediately converted to insoluble form.

One needs to change the soil pH, not the total iron level. An alternative solution is to add the iron in a form which is not readily rendered insoluble - iron chelates (iron in this form is unfortunately relatively expensive).

This interdependence between availability and pH applies to most soil nutrients. It can be shown in diagram form (Figure 2). The issue of nutrient availability is in fact the main reason behind plant sensitivity to pH. Thus vegetables, which grow quickly and need large amounts of the major nutrients nitrogen, phosphorus and potassium, grow best at a pH between about 6.5-7.5. Plants that have trouble collecting enough iron (azaleas, rhododendrons, etc.) grow best at a pH between about 5 and 6.

Figure 2. Nutrient availability verses pH. The higher the graph,
the more nutrients are available.

Controlling pH
If we find our soil is too alkaline (pH too high) can't we lower it by adding an acid? For example, could we add some hydrochloric acid (brick cleaning acid or pool acid)? Conversely, if the pH is too low can we add some sodium hydroxide - caustic soda? The simple answer is no, that will not work - it will either do nothing or it will kill your plants. The problem is a little bit similar to the problem with chemical fertilizers that fully dissolve as soon as applied. Imagine I take 1 litre of distilled water which will be pH 7 - neutral. If I add one drop of hydrochloric acid the pH will fall from 7 to 3. Well, okay, we know hydrochloric acid is a very strong acid, so maybe I just used too much. If one drop per litre gave pH 3 then one drop per 100 litres should give pH 5. True, it will, but then one drop of similar strength caustic soda will take you back to pH 7 and two drops would take you to pH 9! You may be able to get the water to pH 5 using hydrochloric acid but you could never keep it there. The problem is that all the acid is fully expressed. This firstly means that its initial effect is far too severe, and secondly there is nothing in reserve to keep the pH stable against external factors that could change it. So it swings up and down like a yo-yo. Just as with fertilizers, we come up against the concept of buffering. We want the pH not only to be correct but also to stay correct despite perturbing factors. In practice all soils have natural buffering they all resist changes to pH to some degree. The smaller the amount of buffering the easier it is to change the pH, but the more readily the pH will drift away from the desired level, i.e., the less stable the soil. The greater the buffering the more stable the soil but the harder it is to change the pH. That, by the way, is why adding a bit of hydrochloric acid to the soil would probably have no effect the natural buffers in the soil would neutralize it without any significant change to the overall pH.

Just as we discussed before, and for much the same reasons, sands exhibit a low level of buffering, whereas clays and humus rich soils exhibit a high level of buffering. We need more material to change the pH of clay soils than we need for sandy soils. Indeed, in some cases the soil can be so well buffered that it is almost impossible to make any meaningful change to pH. This is especially the case for limestone rich soils which are naturally alkaline.

If we want to make any meaningful change to soil pH we need to use materials which exert a strong buffered effect. They may not push the pH very far, but they exert a lot of force to maintain the change despite other influences. Just as for fertilizers, this implies materials which are expressed slowly. Materials expressed quickly may make a short-term change to the pH but it will tend to drift back as the material added becomes exhausted.

There is a very convenient material we can use to make soil more alkaline (raise the pH) and that is lime. It is rapid in initial action and the effect lasts for quite a long time. Unfortunately the word lime is used for two distinctly different chemicals. Slaked lime or "builders lime" (sold under the name Limil around here) is calcium hydroxide. By contrast, "garden lime" is calcium carbonate. Another similar material often recommended is dolomite, which is a mixture of calcium carbonate and magnesium carbonate. Calcium hydroxide - builders lime - is much more strongly alkaline, and therefore more likely to burn plants and even unprotected skin. Therefore, in principle, calcium carbonate is a better choice. In practice, calcium hydroxide rapidly absorbs carbon dioxide from the air and in the process it is converted from calcium hydroxide to calcium carbonate, so in the long term there is not much difference. (By the way, that is why formulations which call for calcium hydroxide lime, for example Bordeaux mixture, always stipulate that the lime should be fresh.) Nonetheless, garden lime, or (probably even better) dolomite, would be the better first choice for making soil more alkaline.

There is no equivalent material for making soil more acid. Sulphates in general, e.g., ferrous sulphate, magnesium sulphate, aluminum sulphate (hydrangea blueing agent) or ammonium sulphate will all have a fairly rapid acidifying effect but it is not particularly long term. Elemental sulphur lasts longer because it is slowly converted into sulphates by the actions of soil bacteria and water, but for the same reason it is significantly slower in its initial action. A good alternative, however, is to use compost. Compost is naturally acidic and, as stated earlier, improves the buffering of the soil both with regard to pH and also nutrients and water retention.

Gardening is a very rewarding pursuit and you don't need to be a chemist to be a good gardener. Nonetheless, sometimes just a little background knowledge can help to give greater insight and avoid problems that can otherwise lead to much frustration and lost plants. In this way it can make gardening an even more rewarding pastime and hobby.

Mike Hammer has been interested in both science and gardening since early childhood. The former interest was encouraged by his parents and the latter by the privilege of growing up on a 2 acre property which in the 1950s was semi-rural (although now well inside the suburbs). He studied electrical engineering at the University of Melbourne, graduating in 1975 with bachelor's and master's degrees. Since then he has worked as a research engineer and manager for Varian Australia, a high technology manufacturer and exporter of scientific instruments. Mike and his wife, Inge, always dreamed of living on a large property in the mountains but still close to the city. In 1989 a chance remark from a business colleague led them to look into a 6 acre property for sale at Sassafras on Mount Dandenong. It turned out to be the encapsulation of their dream - half temperate rain forest with a creek, and half rhododendron jungle (from plantings in the 1920s and 1930s). Residents there since 1991, they've been happily building a new house and redeveloping the extensive garden.


4.1 Regulation of SOM decomposition and the rhizosphere priming effect

In contrast to our first hypothesis, pine induced a positive RPE and spruce induced a negative RPE on SOM decomposition. The RPE varied between −31% and 47%, which is within the range found in previous studies (Cheng et al., 2014 ). There are at least four hypotheses that can explain why spruce seedlings reduced SOM decomposition, resulting in a negative RPE (a) The concentration of available N was low enough to result in plant-microbial competition for N, leading to suppressed microbial activity and enzyme synthesis (Kuzyakov, 2002 ). (b) Preferential microbial utilization of root C exudates (Cheng, 1999 ), meaning that the microbial community switched its C acquisition from SOM-derived C to energy-rich root-derived C, leading to a concurrent reduction in SOM decomposition (Cheng, 1999 ). (c) Microbial N use was dominated by organic N in the spruce treatment, leading to an underestimated RPE. (d) A distinct opportunistic subset of the microbial community, which grew on root-derived 13 C while at the same time depleting available N, resulted in suppressed activity of microbial SOM decomposers. In our evaluation of these hypotheses below, we find reasons to reject the first three, and conclude that the fourth hypothesis is the most likely explanation for our results.

The RPE has been reported to decrease when inorganic N immobilization exceeds N mineralization (Bengtson et al., 2012 ). Plant competition may aggravate this effect by enhancing the competition for below-ground resources (Dijkstra et al., 2010 ). Since the 15 N recovery in shoots was higher in pots with multiple seedlings than in pots with a single seedling, while gross N mineralization remained constant, competition for N might have contributed to reducing the RPE and lowering the priming efficiency at high seedling density in the pine treatment. However, neither microbial C production (Figure 2B), D incorporation into microbial biomarker PLFAs (Figure 2D), nor potential hydrolytic enzyme activities (Figure 2E) increased in response to cutting the seedlings in the spruce treatment, meaning that plant-microbial competition for N was not the cause of the negative RPE in the spruce treatment.

The second proposed explanation for negative RPEs, the preferential substrate utilization hypothesis, suggests that the microbial community switches its C acquisition from SOM-derived C to energy-rich root-derived C, leading to a concurrent reduction in SOM decomposition (Cheng, 1999 ). This is believed to occur when there is sufficient available N to support microbial growth on labile C compounds (Cheng, 1999 ). However, inorganic N concentrations were lower in the spruce than in the pine treatment. It is, therefore, unlikely that preferential utilization of root-derived C would occur to a higher degree in the spruce treatment. The results further suggest that the negative RPE was not the result of a shift in C acquisition from SOM-derived C to root-derived C by the microbial community as a whole, since a distinct fungal-dominated subset of the microbial community that did not differ between the two species incorporated the most root-derived 13 C (Figure 3A). Water-derived D was incorporated into microbial biomarker PLFAs in a proportion that was more representative of the total microbial community (Figure 3B,C), meaning that most microbes still relied on SOM-derived C for their metabolic processes. These results combined suggest that the preferential substrate utilization hypothesis cannot explain the findings in this study.

The third possible explanation to the negative RPE found in the spruce treatment is that higher microbial assimilation of organic N by micro-organisms (Geisseler et al., 2009 Moreau et al., 2019 ) in the presence of spruce seedlings relative to the control resulted in an underestimated RPE. However, the potential activity of N-targeting enzymes such as LAP did not differ between control and treatments, and was even lower in spruce soil than in pine soil. Therefore, it is not likely that microbial N use was dominated by organic N sources (e.g. amino acids) in the spruce soil but not in the pine soil or control.

We instead propose that a distinct opportunistic subset of the microbial community, which grew on root-derived 13 C while at the same time depleting available N, resulted in negative RPEs by suppressing the activity of microbial SOM decomposers in the spruce treatment. Several of our results support this conclusion. Soil microbes that are responsible for priming are assumed to invest root C exudates into increasing the decomposition of SOM, in order to acquire SOM-derived C and N needed for growth (Hungate et al., 2015 ). A more opportunistic microbial strategy is to grow directly on the root-derived 13 C, without investing it into decomposing SOM in order to release bioavailable C and N. Competition between these microbial strategies can result in the depletion of available N, resulting in reduced SOM decomposition rates (a negative RPE). Our novel SIP method, which simultaneously measure the incorporation of root-derived 13 C and water-derived D, allowed us to separate microbes that grew directly on root exudates from microbes growing on C and N released by SOM decomposition. If competition between these two microbial strategies occurred, we would expect low inorganic N concentrations and high 13 C/D incorporation ratios into PLFAs. Accordingly, both the inorganic N concentration and the 13 C/D incorporation ratio into fungi were higher in the spruce than in the pine treatment (Figure 2C). We hence suggest that opportunistic fungi suppressed microbial decomposer activity by competing for N in the spruce treatment, resulting in a negative RPE. Laboratory experiments (Allison et al., 2014 ), as well as theoretical studies (Allison, 2005 Wakano et al., 2009 ) of interactions between microbial SOM decomposers and such opportunistic ‘cheaters’, have shown that their coexistence is facilitated by spatial separation. The absence of separation leads to gradually increased abundance of cheaters (Allison et al., 2014 ) and reduced abundance and decomposition activities by microbial SOM decomposers (Allison, 2012 Kaiser et al., 2015 ). It is possible that this occurred in the relatively constrained and homogenous pot environment, and while the available N concentrations were still high enough to support the increased activity of SOM decomposers in the presence of pine roots, this was not the case in the spruce treatment.

Fungal and bacterial D incorporation (Figure 2B) as well as inorganic N concentrations (Table 1) were higher in pine soil than in spruce soil, suggesting that fungal as well as bacterial growth rates were higher in the pine treatment. This is to be expected if competition for N occurred in the spruce treatment but not in the pine treatment. Furthermore, as the 13 C/D incorporation ratio of fungi was lower in pine than in the spruce treatment (Figure 2C), the fungal community likely relied on C released during SOM decomposition to a greater extent in the pine treatment than in the spruce treatment. Fungal growth was also higher in pots with intact pine seedlings than in control pots and tended to increase with the number of intact seedlings (Figure 2A,D). The opposite was the case for bacterial growth, and neither fungal nor bacterial growth responded to the presence of seedlings in the spruce treatment (Figure 2A,D). These results combined are in line with our third hypothesis and suggest that fungi were responsible for the positive RPE that occurred in the pine treatment. The observation that fungal decomposition activities and growth on SOM increased in the presence of pine seedlings further emphasize the prominent role of fungi in the decomposition of complex SOM (Nicolás et al., 2019 Yuste et al., 2011 ). However, as discussed above fungi also seemed to be the causative agents of negative RPE induced by spruce seedlings. These contradictory findings highlight the metabolic and ecological diversity of fungi, and suggest that measurements of the biomass and growth of the combined fungal community are not sufficient for elucidating their role in soil C and N cycling.

The vast majority of priming studies have quantified the priming effect using microbial respiration of SOM as a proxy for SOM decomposition rates. Less attention has been paid to how labile C input influences another indicator of SOM decomposition, namely gross N mineralization. Given that both C and N are contained in SOM, there is generally a coupling between SOM respiration and gross N mineralization (Hart et al., 1994 ) and immobilization rates (Barrett & Burke, 2000 ). However, in this experiment the presence of living roots did not influence the gross N mineralization rate, meaning that no RPE on N mineralization occurred even if roots induced RPE of SOM decomposition measured in C units (Table 2). Although soil C and N dynamics are coupled to a large extent, the immobilization and stabilization of C and N in SOM, including the microbial biomass, are at least partially decoupled. Hence, SOM-N can be mobilized independently of C and vice versa. Such decoupling of SOM-C and N mineralization rates in response to labile C input has previously been documented (Ehtesham & Bengtson, 2017 Rousk et al., 2016 ). Proposed explanations include reduced mineralization of N-rich compounds such as chitin and protein (Wild et al., 2018 ) and more efficient microbial use of already available N (Wild et al., 2017 ). Yet another and more speculative explanation for the absence of RPE on gross N mineralization is that there is a finite amount of reactive N groups susceptible to priming and that this N was already depleted at the onset of the experiment. There is also a possibility that the 15 N addition in itself might have resulted in reduced N mineralization rates, due to the relatively low inorganic N concentrations in our soil. However, the inorganic N concentration and daily gross N mineralization rate was still several times higher than the 15 N addition. We, therefore, find it unlikely that the addition had a major influence on the estimated gross N mineralization rates. Regardless of the reason, the results demonstrate that accelerated turnover of SOM in the presence of living roots does not always result in increased mineralization of SOM-N into plant available N.

4.2 Root exudation rates and enzyme activity

We hypothesized that a high density of living roots would result in high root exudation rates, and hence more pronounced RPEs (Bengtson et al., 2012 ). Accordingly, the root exudation rate expressed per gram soil increased with increasing seedling numbers in both the pine and spruce treatment. However, in contrast to the hypothesis, the RPE decreased at higher root exudation rates in the pine treatment, and there was no relationship between the root exudation rate and the negative RPE detected in the spruce treatment. However, soil micro-organisms respond to conditions in their immediate vicinity (Kuzyakov & Blagodatskaya, 2015 ), meaning that root exudation rate per pot or even per gram soil might not be a relevant measure of the conditions at the scale experienced by micro-organisms. If the RPE is controlled by root exudate concentrations experienced by individual microbes, root exudation rates per gram living roots might be a better predictor of the RPE. Accordingly, both priming efficiency (i.e. µg primed-C µg −1 root exudate) and the RPE decreased in pots with multiple seedlings in the pine treatment, probably since the root exudation rate expressed per gram root was reduced by up to almost 50% in pots with five seedlings compared to pots with one seedling (Figure 1B).

SOM decomposition is mediated by extracellular enzymes secreted by soil micro-organisms (Marx et al., 2001 ). The input of labile C substrates can serve as an energy source for the synthesis of such enzymes, resulting in an increase in SOM decomposition (Blagodatskaya & Kuzyakov, 2008 ). Accordingly, changes in extracellular enzyme production, promoted by the addition of labile C, have been suggested as a possible explanation for priming effects. Differences in the potential activity of oxidative and C- and N-targeting extracellular hydrolytic enzymes can, however, not explain why the RPE differed between the two species in this study. The presence of seedlings did not increase potential enzyme activities, and SOM decomposition proceeded at similar rates in pine and spruce soil, despite higher potential enzyme activities of C- and N-targeting enzymes in the pine soil. The concentration of enzymes did therefore not limit the decomposition rate, and was not the cause of different RPEs in the pine and spruce treatments.

The lack of relationship between hydrolytic enzyme concentrations and SOM decomposition suggests that the SOM decomposition rate was limited by the substrate availability rather than enzyme concentrations. Compounds targeted by hydrolytic enzymes might first have to be released from SOM by oxidative enzymes, such as peroxidases and phenol oxidases (Hofrichter et al., 2010 ). Several of these enzymes require constant regeneration of H2O2 by accessory enzymes such as glucose oxidase (Ander & Marzullo, 1997 ). Sugars exuded by plant roots could, therefore, stimulate the activity of enzymes involved in the oxidative decomposition of SOM by providing the substrate for accessory H2O2-generating enzymes, as suggested by Bengtson et al. ( 2012 ). If this is the case and the activity of H2O2-generating oxidases is limited by the concentration of substrate, not the enzyme concentration, this would explain why we did not find a relationship between the concentration of oxidative enzymes and SOM decomposition or RPE in this study. It can also explain the previous observations of first-order or Michaelis–Menten type kinetics of priming (Paterson & Sim, 2013 ). First-order or Michaelis–Menten type kinetics of oxidative SOM decomposition is also partly consistent with our observation that priming efficiency decreased with an increasing number of pine seedlings, since there was a concurrent decrease in the exudation rate per gram root. It does not, however, explain the negative RPE in the spruce treatment. Nevertheless, our results demonstrate that hydrolytic and oxidative enzyme activities are poor indicators of SOM decomposition and the RPE, probably since the assays detect the potential activity of enzymes in a sample, but not the actual enzyme activity in situ (Tiedje, 1982 ).

In this study, we used pots with seedlings that were cut 5 days before the experiment as controls, and not root-free soil like most previous studies. This was an effort to reduce changes in inorganic N and microbial growth, biomass and community composition that occurs over time in an unplanted control, which can confound the effect of root exudates on SOM decomposition. By minimizing the differences in these variables between the control and treatments, the direct effect of root exudates on SOM decomposition can be better understood. The underlying assumptions of the method have been tested and confirmed in a separate experiment, demonstrating that the microbial biomass and community composition, as well as inorganic N concentration and potential enzyme concentrations, were preserved in the control with cut seedlings, but differed significantly in the unplanted control (J. Li & P. Bengtson, unpubl. data). The same experiment showed that 5 days were sufficiently long for root exudation to cease, while at the same time no significant decomposition of dying roots was observed. However, the method is not suitable for species that will still release root exudates after above-ground cutting, or if the aim is to quantify the cumulative RPE over long time periods.

An interesting point in this study is that the potential activities of C- and N-targeting extracellular hydrolytic enzyme were significantly lower in spruce than in pine treatments. The activity and biomass of some microbial groups were also lower in spruce treatments compared to pine treatments. This is surprising, considering that the soil used was a mixture of spruce and pine soil at a ratio of 4:1. Clearly there was no evidence of a ‘home-field advantage’ of microbes in the spruce treatment, but we cannot rule out a ‘home-field disadvantage’ caused by the soil mixture.

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