This section began innocently enough as a simple info blog about jujubes. But during the dormant winter periods with no live action to write about, I went back to my roots (ha!) to write more on soil, biochemistry, and soil microbiology in general. I found myself wanting to keep going, and this blog was becoming less and less jujube-specific.
Thus it made sense to restructure everything.
This blog is now The Biosphere Blog, where I will continue writing about these subjects very dear to me.
(And here is my passion project From Soil to Fruit, a combination of the two and very much a work in progress. This is where topics in this blog are arranged in a more structured book-chapter format, to be explored in far more detail.)
Magnesium (Mg) in soil ranges from about 0.05% in sandy soils up to 0.5% in clay soils. It is more prevalent in clay soils as these contain very weatherable magnesium-containing minerals. Some clay minerals themselves contain magnesium. Magnesium may also be present in some soils as magnesium carbonate (MgCO3) or dolomite [calcium magnesium carbonate, CaMg(CO3)2]. Arid and semi-arid soils may contain large amounts of magnesium as magnesium sulfate (MgSO4).
Availability to Plants
Owing to the presence of magnesium in many soil minerals, its availability to plants is similar to that of potassium, which is also a component of minerals. There is a non exchangeable form (locked away in clay and other particles), an exchangeable form (on the surfaces of colloids), and a form dissolved in the soil water. These three states are in equilibrium, and the largest component is the non-exchangeable magnesium. Of this non-exchangeable magnesium, some is released — as with potassium — when clay particles expand and separate when wetted.
Exchangeable magnesium is about 5% of the total soil magnesium, and this amount along with that in the soil water is the largest contributor of available magnesium to plants. Of the total cation exchange capacity, magnesium is about 4 – 20%. This is much lower than that of calcium (80%), but higher than potassium (up to 4%).
Magnesium ions (Mg2+), as with calcium ions (Ca2+), are readily leached from soil. In many soils, the rate of weathering of magnesium-containing minerals can balance this removal, but in sandy soils with little clay, removal by leaching will predominate and magnesium will be found in higher concentrations in the subsoil.
The Australian soils which tend to be low in magnesium are those in high rainfall areas, and especially in the coarse-textured acid soils near the coast.
Magnesium in Biochemistry
A magnesium atom is at the heart of every chlorophyll molecule and thus essential for both the synthesis of chlorophyll as well as in photosynthesis. Below is the structure of chlorophyll a, and the structures of the other (similar) chlorophyll variants are here.
Magnesium also features in many enzyme reactions, and in all the ones that use or synthesise adenosine triphosphate (ATP), as ATP must bind to magnesium to become biologically active. Mg2+ also binds to and strengthens the structures of DNA and RNA. Magnesium, as with calcium, is also important in strengthening cell walls and in cell membrane stability and permeability.
Magnesium Deficiency Symptoms
Mg2+ ions have a higher concentration in soil water than potassium ions (K+), but uptake of Mg2+ is lower than of K+. An excess of K+ can thus severely interfere with the uptake of magnesium, as can other cations (positively-charged ions) such as ammonium (NH4+).
Magnesium uptake is also reduced in acidic soils, but this is not so much due to the increase of H+ ions, but because the increased availability of aluminium ions (Al3+) interferes with Mg2+ uptake.
Magnesium deficiency symptoms can vary between species, but there are also general similarities. For example, as with potassium ions (K+), Mg2+ is very mobile within a plant, and can move from older to younger leaves. Deficiencies will show up in older leaves first as a result.
Interveinal (between the veins) yellowing occurs as chlorophyll breaks down and is not replaced (chlorosis). Necrotic (dead) spots may appear in these yellow regions in extreme deficiencies. Plants exposed to strong sunlight may take on a wilted appearance, and individual leaves may become stiff, brittle, and fall off prematurely.
Magnesium Toxicity Symptoms
Magnesium toxicity is rare, and it’s more likely that high amounts of magnesium will induce a calcium deficiency rather than a magnesium toxicity, by interfering with the uptake of Ca2+ ions.
There is actually a balance between Mg2+, Ca2+ and K+ ions and their uptake from soil, due in part to their positions on the Periodic Table. These are all positively-charged elemental ions close to each other on the Table, and have similar properties because of this.
Magnesium and calcium are elements 12 and 20 respectively on the Table. Both are in the Group 2 column, meaning they both form 2+ ions. Magnesium is immediately above calcium, and is a much smaller atom, with 12 protons compared to calcium’s 20. In very simple terms, this makes a Mg2+ ion much easier to uptake than a Ca2+ ion.
Potassium is element 19, with just one proton less than calcium’s 20. This makes it only slightly smaller in size, but it is a Group 1 element with a charge of 1+ compared to calcium’s 2+. Potassium ions are rapidly taken up by plants while that of calcium ions is slow. Potassium ions, as mentioned above, can also interfere with the uptake of magneisum.
It might be worth discussing this balance between the three, and the chemistry, in deeper detail in a separate post. But certainly the take-home message here is that there is a balance, and that growth of plants will be affected should any of the three nutrients be significantly out of balance.
Elemental calcium (Ca) makes up 3.64% of the Earth’s crust, making it the fifth most common element in the crust after oxygen (O), silicon (Si), aluminium (Al) and iron (Fe). This makes it the most abundant of all plant nutrients after oxygen and iron. In dry plant tissue, calcium ranges in concentration from 5 – 30 mg per gram.
Availability to Plants
Calcium in soil comes from weathered rocks, and the amount of naturally-occurring calcium will depend on the parent rock, how much that rock has weathered, and how much leaching has occurred. For example, limestone-derived soils are usually very rich in calcium, present as calcium carbonate (CaCO3). Yet their surfaces may be low in calcium where leaching has been high. Old, weathered soils in wet environments may be very low in calcium due to excessive leaching, while in arid regions calcium may accumulate in the upper soil in the form of gypsum (calcium sulfate dihydrate, CaSO4.2H2O).
Soils high in calcium carbonate are high in pH (alkaline), and calcium ions (Ca2+) when in the presence of high pH tend to form Ca-humus complexes. These give such soils a dark colour.
Low pH (acid) means the presence of H+ ions, and these increase the weathering of calcium-containing rock minerals, which releases calcium ions into the soil. H+ ions also exchange two-for-one with Ca2+ ions on soil colloids, which releases the latter into soil. These calcium ions will leach in wet climates, the rate of leaching increasing with increasing rainfall and increasing amounts of calcium-containing minerals. 200 to 300 kg of calcium per hectare typically leach from temperate soils!
Weathering of rock minerals which contain carbonates (CO32- ions) is very dependent on the presence of carbon dioxide (CO2) in the soil. Calcium carbonate (CaCO3) is a rather insoluble compound, with just 10 – 15 mg Ca dissolving per litre of water. But in the presence of CO2, the much more soluble calcium bicarbonate [Ca(HCO3)2] is formed:
CaCO3 + CO2 + H2O → Ca(HCO3)2
Ca(HCO3)2 dissociates into calcium (Ca2+) and bicarbonate (HCO3-) ions in the soil water and become prone to leaching.
Surprisingly, adding organic matter can also increase the leachability of calcium. As the organic matter decomposes, CO2 is released into the soil. This is converted into carbonic acid (H2CO3) which dissociates into bicarbonate (HCO3-) and H+. H+ ions, as mentioned above, can exchange two-for-one with Ca2+ ions on soil colloids, which again releases Ca2+ ions into the soil where they are subject to leaching.
The formation of nitrate (NO3-) also affects the availability of calcium. Going back to the nitrogen cycle, nitrate forms from ammonium (NH4+) via nitrification:
2NH4+ + 4O2 → 2NO3- + 4H+ + 2H2O
This process also produces H+ ions. A H+ ion is a H+ ion, and whether from nitrification or carbonic acid dissociation, is equally capable of displacing calcium ions from colloids no matter what the source. H+ ions are produced at a greater rate from nitrification than from carbonic acid dissociation however, and this has implications wherever ammonium fertilisers are applied. Such fertilisers, through nitrification, will not only acidify the soil (acidity is a direct result of the concentration of H+ ions) but those same H+ ions will increase the removal of calcium from soil via leaching.
It follows that climatic factors that affect nitrifying microbes, such as moisture and temperature, will also affect nitrification and the rate of calcium leaching (and acidification). This is why soils in warm, humid environments (the tropics especially) naturally increase in acidity with year-long exposure of microbes to warm, wet conditions and plenty of lush green (nitrogen-rich) fallen vegetation. This abundance of organic matter also leads to the formation of carbonic acid and yet more H+ ions as described above.
Some soils high in organic sulfur may also become more acidic as this sulfur is converted into sulfuric acid.
Acidification may also increase in the presence of increased root production, as roots can excrete H+ ions in the presence of ammonium (NH4+).
Fossil-fuel burning leads to the formation of acids such as sulfurous acid (H2SO3), sulfuric acid (H2SO4), nitrous acid (HNO2) and nitric acid (HNO3). All of these precipitate out of the atmosphere and into soil, where they rapidly break down soil minerals via chemical action and acidify the soil in the process.
Whether naturally-caused or man-made, it’s clear that soils will generally trend towards a slowly-increasing acidified state. Increasing acidification not only contributes significantly to soil degradation (for many reasons best covered in a future post), it also renders many nutrients either unavailable to plants or at toxic levels. And as soils accumulate more H+ ions, those ions will displace calcium, and those calcium ions will leach away in the presence of water.
A time-honoured way of ensuring calcium remains in soil, is accessible to plants, and slows the natural acidification of soil is to apply liming materials, which are both calcium-rich and very alkaline. Crushed limestone or chalk (both of mostly calcium carbonate) are the primary sources of ‘agricultural lime’. In fact, this artificial application of alkaline materials to soil by people is the only way a soil’s pH can be raised and calcium leaching reduced. As mentioned above, soils naturally become more acidic with time, and lose calcium when wetted.
The above may sound like soils are doomed to forevermore deplete in calcium without human interference, but in reality there is a calcium cycle in nature that returns calcium to soils — it is only our intensive agricultural practices that place a heavier load on the land. I’d like to cover this cycle in a future post.
Liming, and the importance of calcium to soil structure, also is very much the subject of a future post — I’m already getting carried away with the chemistry enough as it is! But it should be quite apparent that calcium is more than just a nutrient, and has a multifaceted role when it comes to soil.
Calcium in Biochemistry
Calcium is needed for cell elongation and cell division and has important roles in cell wall strength, and cell membrane stability and permeability. (Note: plant cells have an internal cell membrane and an outer cell wall. The cell wall provides structural strength. Animal cells only have a cell membrane.)
A strong cell wall is more resistant to attacks by insects and the enzymes secreted by many bacteria and fungi intended to pierce cell walls. Calcium helps maintain the structural integrity of cell membranes by regulating the ions that leave and enter cells and ensuring membranes don’t become too ‘leaky’.
Calcium has roles in enzyme and hormone processes, and helps in transpiration and heat regulation by regulating the pores in leaves called stomata (plural form of stoma).
Calcium Deficiency Symptoms
Reduced growth is one sign of a calcium deficiency as this mineral is vital in the elongation and division of cells. Calcium is not mobile in a plant, and thus a deficiency first appears in the growing tips and the youngest leaves. The leaves become deformed, chlorotic (become yellow from a lack of chlorophyll production), and at an advanced stage show necrosis along the leaf margins (edges). Affected tissues become soft as the cell walls weaken.
Growing root tips are especially affected and will die in severe cases. This has consequences for the entire plant as it is only the growing tips that are able to take up calcium ions. Anything preventing the tips from growing, such as temperature, moisture content, or soil quality, will also reduce calcium uptake.
An absolute calcium deficiency as described here is actually quite rare, but deficiencies will likely show in the fruit and storage tissues where calcium is under-supplied to a plant. Blossom-end rot of tomatoes and bitter pit in apples are two such examples. These arise as calcium is only moved through a plant via the xylem (the dedicated transport tissue in a plant, which moves water from the roots to the stems and leaves via capillary action). If the xylem sap is low in Ca2+, fruits being last in line to receive this sap will be the first to suffer.
High amounts of potassium (K+) and magnesium (Mg2+) will interfere with calcium uptake, even if Ca2+ is of sufficient amounts. Calcium should be applied at the same time if high amounts of K+ and Mg2+ are applied as fertilisers. High applications of ammonium fertilisers can acidify the soil and lead to leaching of calcium away from plant roots. Sodic soils, those containing high amounts of sodium ions (Na+) attached to clay particles (not to be confused with saline soils, those with salty soil water) also restrict Ca2+ uptake.
High applications of phosphorus will cause Ca2+ to react with excess phosphate (PO43-) and form insoluble calcium phosphate [Ca3(PO4)2], thus locking calcium away.
Calcium Toxicity Symptoms
Calcium toxicity does not exist, but soils with high levels of calcium carbonate will have a high pH, and it is this high pH that may cause problems if the supply of other nutrients is affected.
So far we’ve covered he big three macronutrients: nitrogen (N), phosphorus (P), and potassium (K) — the famous NPK. Today we’ll cover a lesser-known, but also important nutrient for plants: sulfur (S).
It may surprise you that sulfur is an essential macronutrient — most people think of sulfur as the pure yellow powder in long-ago school science labs, or maybe as a component of hydrogen sulfide (H2S), or ‘rotten egg gas’. Yet sulfur has a very important role in both animal and plant biochemistry, which we shall see.
Availability to Plants
Temperate soils contain 0.005 – 0.04% total sulfur, and those with more organic matter tend to hold more sulfur. Total sulfur in dry plant tissue is around 0.2 – 0.5%.
Sulfur exists in soil in both organic (with carbon) and inorganic (without carbon) forms.
The inorganic form is mostly as sulfate ions (SO42-), and it is in this form that sulfur is mostly absorbed by plants.
In dry soils, sulfate ions combine with calcium (Ca2+), magnesium (Mg2+) and sodium (Na+) ions to form salts [calcium sulfate (CaSO4), magnesium sulfate (MgSO4) and sodium sulfate (Na2SO4) respectively]. (Magnesium sulfate is also known as ‘Epsom salt’, after a saline spring in Epsom, Surrey, England.)
These salts can build up to high levels in the upper soil layer under dry conditions. In wet conditions however, sulfate ions are either loose in the soil water or bind to colloids. Sulfate ions in these conditions enter an equilibrium between soil water and colloids as does phosphorus in the form of phosphate, and becomes exchangeable sulfur. Sulfate’s ability to adsorb to colloids decreases with increasing soil pH and increases with increasing clay content. Large amounts of loose sulfate ions may leach in the increased presence of water.
Some sulfur enters the soil via the atmosphere as sulfur dioxide (SO2). This is a natural part of the sulfur cycle, but burning of fossil fuels has increased atmospheric levels of this gas significantly. (I’d like to cover the sulfur cycle in more detail in a future post.)
Organic forms of sulfur can come from manures and dead plant and animal material, and is made available to plants via microbial activity. In anaerobic conditions (absence of oxygen), this organic sulfur is metabolised (’eaten’ and converted) by chemotrophic (’nourishment from chemicals’) sulfur bacteria into hydrogen sulfide (H2S). If anaerobic conditions persist, this hydrogen sulfide is then further converted into elemental sulfur (S) by the photosynthetic green and purple bacteria. (These bacteria utilise H2S instead of H2O (water) in the presence of photons to make glucose, producing pure sulfur rather than oxygen gas (O2) as the by-product. These anoxygenic photosynthesisers were Earth’s first photosynthesisers and were very briefly mentioned in A Crash Course in Photosynthesis .)
In aerobic conditions (presence of oxygen), H2S auto-oxidises into sulfate (SO42-) and is also converted by the same chemotrophic sulfur bacteria mentioned above into sulfuric acid (H2SO4). Elemental (pure) sulfur (S) can also be converted into sulfuric acid by lithoautotrophic (’self-nourishment from rocks’)* bacteria of the genus Thiobacillus.
* Lithoautotrophs extract energy from minerals to ultimately make their own food (glucose), while photoautotrophs (more commonly known as photosynthesisers) extract energy from photons (light) to do this.
The sulfuric acid molecules dissociate into H+ and SO42- ions in the soil water. The SO42- ions becomes available to plants and the soil becomes more acidic from the additional H+ ions. (This is why sulfur is traditionally applied to alkaline soil to lower the pH.)
Cysteine and methionine are the two most important sulfur-containing amino acids in plants. As plants must make these for themselves, it is vital that sulfur be available, hence why this is a macronutrient.
In extremely simplified terms, sulfate reacts with ATP to form cysteine, the first stable sulfur-containing organic (contains carbon) compound made by a plant. Through still more reactions, cysteine is converted to methionine.
Both cysteine and methionine participate as free acids in other reactions — cysteine is a precursor in the making of vitamins and antioxidants, while methionine is a precursor in the making of glutathione (an antioxidant) and the plant hormone ethylene.
Both, as amino acids, are also essential in the formation of proteins and enzymes (which are also proteins). But cysteine (not methionine) has an additional role in that it helps proteins fold into their correct shapes via disulfide bridging — an S-S bond that forms a bridge between two molecules.
Here are two cysteine molecules joined together via an S-S bridge:
This following image represents a string of amino acids — a protein in other words. Cysteine molecules along this protein will form disulfide bridges with other cysteine molecules in other locations along the molecule, causing the protein to fold in a particular way.
Different proteins will fold in their own unique ways, determined by where cysteine amino acids in each protein are in relation to each other.
Correct protein folding is extremely important in biochemical reactions — as enzymes are proteins, and many reactions depend on enzymes, those reactions simply won’t occur, or will produce faulty end products, if the enzyme’s shape is ‘wrong’. Cystic fibrosis and sickle cell anaemia in humans are classic examples of incorrect protein folding. These are both genetic diseases, each caused by just one faulty protein not folding correctly [cystic fibrosis transmembrane conductance regulator (CFTR) protein in sufferers of cystic fibrosis, haemoglobin in sufferers of sickle cell anaemia].
Sulfur Deficiency Symptoms
A deficiency of sulfur will prevent cysteine and methionine synthesis, which in turn prevents crucial proteins and enzymes from forming.
Chloroplast formation is affected, which reduces photosynthetic activity and sugar production. A lack of essential proteins and enzymes in general leads to stunted growth overall. The growth of shoots is more affected than the growth of roots, and plants tend to be rigid, brittle, and with thin stems.
Unlike nitrogen, potassium and phosphorus deficiencies, a sulfur deficiency appears in the youngest leaves first. This implies that sulfur is not as mobile in plants as the other three macronutrients — sulfur here is ‘locked away’ in proteins and a plant must rely on uptaking sulfate from the soil for continual protein production.
The topmost affected leaves will change colour from a light green to become more and more yellow as chloroplasts degrade, followed by leaves further and further down. The internode length (the distance between nodes along a stem or branch) may decrease as growth decreases.
Sulfur Toxicity Symptoms
Plants are not sensitive to high levels of sulfate in the soil, except where there are high concentrations in saline soils. Here, the effects of reduced growth rate and dark green leaves are not specific to a sulfur excess so much as they are more typical of salt-affected plants in general.
Plants can absorb some sulfur dioxide (SO2) through their leaves without harm, but high concentrations such as around industrial areas can be toxic. SO2 dissolves in the moist leaf tissue and forms sulfurous acid (H2SO3), which dissociates into H+, HSO3- and SO32- ions. These ions, along with SO2, disrupt chloroplast membranes and interefere with photosynthesis processes generally. This toxicity presents as necrotic (localised, dead) tissue in leaves.
Elemental phosphorus (P) makes up 0.02–0.15% of soil, and primarily exists as hydrogen phosphate (HPO42-) and dihydrogen phosphate (H2PO4-) ions. These are both simply called phosphates (orthophosphate ions to be more specific), and are anions (negatively-charged ions).
Australia’s very old soils are typically low in total P. Phosphorus is not mobile in soil and is best applied close to the roots, but as phosphorus tends to remain in the upper soil there is also a risk of run-off during heavy rainfall.
As with soil potassium ions, the phosphate ions exist in three soil fractions: those dissolved in the soil water, those attached to colloids and which are in equilibrium with the soil water, and those locked away in soil minerals until released slowly due to weathering.
HPO42- is almost absent at pH 5 (acidic) but both ions are in roughly equal amounts at pH 7 (neutral). On the other hand, H2PO4- is the one to decrease in concentration as pH increases (and the soil becomes more alkaline).
This is because the two ions enter an equilibrium dictated by the presence of hydrogen ions (H+):
HPO42- + H+ ↔ H2PO4-
In the presence of more H+ (a more acid pH), HPO42- ions in the soil will take up those H+ ions to form H2PO4- ions. (And the equation shifts to the right.) The concentration of HPO42- drops to virtually zero in very acidic soil as they have mostly formed H2PO4- ions.
In more alkaline environments however, where there are less free-floating H+ ions available, H2PO4- ions are more likely to give up H+ ions into the soil water and form HPO42- ions. (The equation shifts to the left.) However, this doesn’t necessarily mean that those HPO42- ions become more available, especially in very alkaline soils as we’ll see shortly.
Overall, phosphorus solubility is very pH-dependent in soils. If most of the available phosphates are attached to colloids, an increase in pH will help those phosphates detach and enter the soil water. pH also becomes a factor in the rhizosphere (the region immediately surrounding the roots), which can be as much as one unit of pH higher or lower than the surrounding soil. This really needs to be the subject of a separate post, but this difference in pH is due to whether nitrate or ammonium is the dominant nitrogen nutrient, which influences whether anions (negatively-charged ions) or cations (positively-charged ions) are uptaken in higher amounts, which in turn determines the amount of H+ ions near the roots, which determines pH. In short, an increase in rhizosphere pH should enable more phosphate to detach from colloids and become more available to roots.
Going back to the highly alkaline soils though, such soils typically have high levels of carbonate (CO32-) and bicarbonate ions (HCO3-). Soluble phosphate availability decreases in calcareous soils [those containing calcium carbonate (CaCO3)], as phosphate and calcium ions (Ca2+) combine to form calcium phosphate [Ca3(PO4)2], which is not very soluble in water. Soluble phosphate availability also decreases in alkaline soils generally as phosphate preferentially binds to soil colloids when there are very few H+ ions available. In both cases, phosphate ions are inaccessible, either as calcium phosphate or on soil colloids.
Similarly, phosphates form insoluble compounds with iron and aluminium in very acidic soils which lowers their availability in those. [Iron phosphate can exist as iron (ferric) phosphate (FePO4) or iron (ferrous) phosphate (Fe3(PO4)2). Aluminium phosphate is AlPO4.]
An interesting, biological (biotic), route by which phosphate becomes available to plants is via the hyphae (long filaments) of endotrophic (literally ‘nourishment from internally’, but here meaning ‘living inside root cells’) mycorrhizae (plural form of mycorrhiza, ‘root fungus’). In exchange for sugars from photosynthesis, mycorrhizal fungi provide the plant with phosphorus (and often water and other nutrients). The long, exploring hyphae of the fungi are in essence an extension of a plant’s roots, but finer and further in their reach.
Organic Phosphate Compounds
Phosphorus is uptaken as inorganic phosphates, ie in compounds that do not contain carbon — hydrogen phosphate (HPO42-) and dihydrogen phosphate (H2PO4-). Once inside a plant however, phosphorus rapidly becomes incorporated into organic phosphates, ie ones that do contain carbon. Many of these are the phosphorylated sugars and alcohols. Sugars and alcohols contain only carbon (C ), hydrogen (H) and oxygen (O); phosphorylated ones have a phosphorus atom as well. These compounds are mostly intermediaries in many metabolic reactions — they don’t have an end purpose per se, but rather are the intermediate products of reactions that then feed into other reactions until some end product is finally made.
By way of example may I refer you yet again to this image, and specifically the left-hand side where compounds with the words ‘phosphate’ and ‘phospho’ feature heavily. None of these are standalone molecules; they are all intermediaries in a series of reactions by which glucose (a simple sugar) is ultimately converted into pyruvate (a compound essential in cellular respiration).
And just by way of illustration as to what a phosphorylated anything looks like, let’s take the first two molecules in that reaction: glucose and glucose 6-phosphate. This is glucose, comprised only of carbon, hydrogen and oxygen. Each carbon atom is numbered 1 to 6 so chemists and biochemists can refer to specific ones:
And this is a phosphorylated glucose, glucose 6-phosphate (here a chemist/biochemist can tell immediately from the name that the phosphate ion is attached to carbon number 6, and derive its structure accordingly):
Adenosine Triphosphate (ATP)
Phosphorylation is a very important process in biochemistry, and one very important end product from phosphorylation is adenosine triphosphate (ATP). ATP was first mentioned in the discussion on nitrogen, and here it is again to show, this time, the three phosphorus atoms/three phosphate ions:
ATP is the energy carrier that powers cellular processes, and is absolutely essential to all life no matter how simple or complex.
Not only is nitrogen essential for the formation of this molecule, but so too is phosophorus.
DNA and RNA
Another place where phosphorus end up is in the backbone of DNA and RNA. Here is DNA (RNA is more or less a single-stranded version of this) showing the phosophorus atoms in yellow. Each phosphorus has four oxygens attached to it, making this a phosphate group.:
DNA and RNA are essential for the formation of proteins and enzymes, which are vital for cellular processes, growth and reproduction.
Phosphorus Deficiency Symptoms
Plant deficiencies will generally occur once the concentration of P in dry weight matter falls below 0.2%.
Having seen phosphorus’ importance in ATP, DNA and RNA, it should be no surprise that phosphorus-deficient plants show stunted growth. The dry matter shoot:root ratio is also typically low. P-deficient fruit trees often exhibit a reduced growth rate of new shoots and a poor development and opening of buds. Fruit and seed yields are often low and of poor quality. New leaf size and numbers of new leaves may be small.
As with nitrogen and potassium, phosphate too is highly mobile in plants. Again as with nitrogen and potassium, symptoms first appear in older leaves, as phosphate moves not only up into young leaves, but down as well into growing root tips. Older leaves stripped of phosphates take on a dark green colour, even becoming blue-green in some species. Fruit tree leaves may be tinged with a brownish colour. This colouration is due to a buildup of excess carbohydrates that are converted into purplish pigments called anthocyanins.
Phosphorus Toxicity Symptoms
Plants will show stunted growth, and even die, in the presence of too much phosphorus too. Toxicity is more pronounced within a pH range of 5 to 7, where phosphates are more likely to be in a soluble state in the soil water. Large applications of poultry manure, higher in phosphorus than other manures, can cause toxicity especially on sandy soils which cannot absorb phosphate ions as readily as more colloidal soils.
Excess phosphate in soil will form insoluble compounds with iron (iron phosphate) and zinc [zinc phosphate, Zn3(PO4)2], leading to deficiencies in these.
Phosphates are not very mobile in soil. Plants will not uptake any more phosphate than they need, and thus additional applications will tend to accumulate in the upper soil, exacerbating the onset of toxicities. As phosphates tend to attach to soil particles, heavy runoff and associated erosion can send excess phosphorus to river or other water systems. Phosphorus, along with nitrogen, is a limiting nutrient in water, thus phosphate- and nitrogen-rich fertilisers that enter waterways will produce algal blooms.
Phosphorus is very much a nutrient for which ‘if some is good then more is better’ definitely does not apply.
Last week we explored why nitrogen is an essential macronutrient in plants, by looking at the molecules it appears in, and the biochemical processes relying on those molecules. From that we could better understand where and why nitrogen deficiencies and toxicities can arise.
This week we shall look at elemental potassium, or K [from the Latin word kalium (’potash’, from where the word ‘potassium’ itself comes), from the Arabic al-qaliy (’the ashes, burnt ashes’, and from where we also get alkali)]. We’ll examine how it becomes available to a plant, and where it appears in a plant. From that we’ll learn what the symptoms of a deficiency are.
Availability to Plants
Potassium makes up about 2.3% of the Earth’s crust, mostly as the components of clay and other rock minerals. Potassium ions (K+) are positively-charged (cations) and thus adhere strongly to the negatively-charged clay and humus colloids in soil. These ions are very soluble, thus soils rich in clay — which can hold onto these ions — tend to be rich in potassium, while very sandy soils — which can’t — are very poor in potassium.
Potassium in soils is not always available to plants however. Some of it is locked away irretrievably in rock minerals, but does become available gradually over time as the minerals break down and slowly release potassium into the soil water. Some potassium is trapped between the sheets that make up clay particles but is slowly released as these expand and separate when wetted. ‘Poverty in the midst of abundance’ can apply in these situations.
The most readily-available potassium is that on the surfaces of colloids and the potassium ions already dissolved in the soil water. As ions in the soil water are uptaken by plant roots, more ions on colloid surfaces are released to take their place. Excess ions in the soil water can reattach to colloids, and an equilibrium becomes established between the concentrations in the soil water and on colloid surfaces. This is called exchangeable potassium.
The more moist a soil, the more potassium can enter the soil water and be uptaken by the roots, but at the same time very wet conditions increase leachability.
Meristematic cells in plants are akin to the stem cells in animals, in that they too are undifferentiated (unspecialised) cells that undergo cellular division and form (differentiate) into specialised tissue such as leaves, flowers and roots. Potassium is essential for this task of producing sturdy stems, well-developed flowers and strong roots. It aids in loosening cell wall material (essential for cell expansion to occur) and regulates phytohormones (’plant hormones’) such as indole acetic acid (IAA) and cytokinins (more nitrogen-containing compounds) which then initiate that cell division.
Strengthened Cell Walls and Disease Resistance
Potassium strengthens cell walls by thickening them. Nitrogen produces a growth spurt, and potassium strengthens that growth spurt.
Strong cell walls are more resistant to pests and diseases in that it is much harder for insects and fungi to penetrate those walls.
Water Movement and Cell Turgor
Potassium enables the uptake of water by cells and tissues. This increases cell turgor, or rigidity, which is essential for cell expansion in young tissue and a strong plant overall. Turgor is also important for the correct opening and closing of the pores in leaves called stomata (plural form of stoma). These are the entry points for carbon dioxide and the exit points for oxygen during photosynthesis. The stomata also allow excess water to leave a plant via transpiration and minimise water loss by closing when conditions are hot and dry. A plant with weak stomata cannot control gaseous exchange efficiently and is more likely to wilt.
Photosynthesis, Sugar Movement and Fruit Development
Potassium has indirect and direct importance in photosynthesis. We’ve seen how it regulates the closing and opening of stomata; it also has a role in the diffusion of carbon dioxide from the atmosphere into the chloroplasts. Potassium also facilitates the movement of photosynthates (products of photosynthesis, or sugars) around the plant via the phloem (specialised tissue for the transportation of sugars).
Potassium not only assists in the translocation (transport process) of newly-made sugars, but also helps mobilise stored proteins in leaves and stems. This ensures the formation of well-developed flowers and fully-formed, sweet, juicy fruits with a longer shelf-life.
Enzyme Activation and Cation-Anion Balance
Potassium as a nutrient doesn’t form molecules as others do, and exists solely in ionic form, ie as K+ ions. The main function of K+ in biochemistry generally is to act as a catalyst in the activation of enzymes, and in plants potassium catalyses over 60 enzymes to do with plant growth. Potassium also catalyses enzymes involved in regulating the rate of photosynthesis and the production of ATP.
Potassium, being an ion, regulates the cation-anion balance in plant tissue and the rhizosphere (the region surrounding the roots where microbiological and chemical processes are influenced by the roots).
Potassium Deficiency Symptoms
Depending on species, elemental potassium makes up 1.5–6% of dried plant tissue by weight, and deficiencies will appear below this concentration. As with nitrogen, potassium is highly mobile within a plant, and deficiencies show first in the older leaves as potassium is redirected to newer, growing leaves.
In most plants a deficiency first begins with a reduced growth rate, followed later by chlorosis (the insufficient production of chlorophylls resulting in yellowing leaves) and necrosis (localised death of cells) along the leaf margins (edges) and tips. These are similar to nitrogen deficiency symptoms, but occur very early for potassium rather than very late as for nitrogen.
Root, flower, and fruit development are typically reduced in potassium-deficient plants. Turgor decreases and plants become less drought-tolerant and wilt easily under water stress — symptoms can actually be confused for drought.
Plants deficient in potassium are also more susceptible to frost damage, insect and fungal attack, and saline conditions.
When the nitrate:ammonium ratio in soil is low, excessive amounts of ammonium interfere with the uptake of potassium to cause a deficiency.
Potassium ‘Toxicity’ Symptoms
There is no such thing as potassium toxicity, but excessive amounts of potassium can interfere with the uptake of magnesium (Mg) and calcium (Ca), causing deficiencies in those. The reverse also applies, in that excessive amounts of either can cause deficiencies in the others. These are all cations (positively-charged ions) and compete for uptake by a plant.
Macronutrients are those a plant requires in high concentrations. There are six of these: nitrogen (N), potassium (K), phosphorus (P), magnesium (Mg), calcium (Ca), and sulfur (S).
Plants receive these nutrients either as standalone ions or as part of other compounds. Potassium, for example, is available to plants as potassium ions (K+), while nitrogen is only available to plants as ammonium ions (NH4+) or nitrate ions (NO3-).
Elemental nitrogen (N) is about 2–5% by weight of dry plant tissue, depending on species. This doesn’t seem like much, especially when compared to the carbon and oxygen contents of 40–45% each (these are high as carbon and oxygen are major components of sugars, starch and proteins). Yet deficiencies may appear when this concentration falls below 1.5–2%. Nitrogen is the highest in concentration of all the macronutrients before deficiencies begin to appear, with the next highest being elemental potassium (K), at around 1–1.5%.
To find out, let’s first explore all the places nitrogen appears in a plant, and from that, understand why it is so important. From this we can determine which deficiencies and toxicities arise, and wrap up with how to recognise the symptoms of both.
Nitrogen atoms are essential to the structure of chlorophylls, the compounds in chloroplasts which use light energy to split water into hydrogen and oxygen during photosynthesis. There are several different types of chlorophyll: chlorophyll a below is the one common to all oxygenic photosynthesisers.
Four nitrogen atoms (N) surround a magnesium (Mg) atom (and one reason why magnesium is an important macronutrient too). This chlorin ring structure at the top of this molecule is the photosensitive part and is common to all the chlorophylls. The long tail is a hydrocarbon [made of hydrogen (H) and carbon (C ) atoms only] which anchors the entire molecule inside the chloroplast membrane.
Just an aside whilst here, it is very common in chemistry to not write ‘C’ for the carbon atoms in structural formulae — as carbon exists in so many things this saves a lot of time (and printed space - it all adds up when some of these organic compounds are very large)! Thus when you see something like:
‘read’ it as:
And once you add the carbons in, you have to then add the hydrogens where appropriate (as above) so the valency for each carbon atom is always four…it’s all so tiresome!
Amino Acids and Proteins
Proteins are both the structural components in plants as well as enzymes (biological catalysts essential in many biochemical reactions). And proteins are made up of amino acids. Just as all chlorophylls have a common chlorin ring structure, so too do amino acids have a common structure, depicted generically as:
where the R group is the variable part (the letter ‘R’ was chosen as it is not used for any element in the Periodic Table and thus can’t be mistaken for one). You can see all twenty versions of the R group here, each of which makes a unique amino acid. (Fun story: once upon a time I could actually write every single one of these from memory — and tell you which RNA codons coded for each of these — not anymore!)
Every single amino acid has the nitrogen-containing amine (-NH2) group in common, regardless of the R group (some of which also contain nitrogen).
Adenosine Triphosphate (ATP)
ATP, or adenosine triphosphate, is the molecule that provides the energy that drives many, many biochemical reactions. It is found in all life, from the most ancient bacteria, to plants, to animals. In A World Without Prokaryotes I linked to this image just as an FYI to show what cellular respiration is, deliberately not providing further explanation as it’s incredibly involved and wasn’t relevant to the discussion. (Though I may pick it apart one day for anyone who’s interested.)
I never mentioned ATP there, but here I link to that image again to make the point as to how vital ATP is in cellular functions. Look how many times it is needed, and just look at all those nitrogen atoms in the diagram below! (That is actually very significant when it comes to energy, and a reason all explosives are also very nitrogen-rich.)
Nucleic acids are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), of which there are three types: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).
DNA codes for genes, mRNA translates those genes into amino acids, and tRNA transfers those amino acids to cellular structures called ribosomes, where rRNA assembles those amino acids into proteins and enzymes.
(Yes, that’s really all there is to it! DNA is nothing more than a set of instructions on how to assemble amino acids together. But it’s the proteins those amino acids then form that determine everything else and make an organism ‘go’.)
DNA is made of four bases: cytosine (C ), guanine (G), adenine (A) and thymine (T). RNA has the first three, but the fourth base is uracil (U) instead of thymine. Again, have a look at all that nitrogen!
[With reference to the diagram above: RNA usually exists as a single-stranded molecule folded back onto itself (folding not shown here), rather than the famous double-stranded helix of DNA.]
Growth and Reproduction
A growing plant uses proteins and enzymes to grow additional cells that then differentiate into roots, branches, leaves, flowers, fruits and seeds. These cells come from cellular division, which is where one cell divides in two to make two copies of itself, each of which creates another two copies, and so on. Each copy contains identical DNA, which itself had divided and copied itself into each cell during division.
The specialised sex cells (pollen and ovules) also form from (a different type of) cellular division which also requires additional production of DNA and proteins.
Thus growth and reproduction are also heavily dependent on nitrogen, simply because of the extra DNA and proteins that must be formed to make the cells.
From all this it’s pretty clear that nitrogen features prominently in all life processes of a plant! It is required for photosynthesis, amino acid and protein synthesis, DNA replication, growth and reproduction, and as a major component of the energy-providing ATP molecule.
Nitrogen Deficiency Symptoms
All these functions is why nitrogen is by far the most important macronutrient for plants, and it follows that a lack of nitrogen — even starvation — would limit these functions noticeably.
Yet it’s because nitrogen features in so many different processes that a nitrogen deficiency is surprisingly hard to diagnose. This is because these processes involve complex pathways to get from beginning to end, and a disruption anywhere along a pathway by some other, different, factor can lead to the same visual syndromes.
For example, stunted growth would be a very obvious first sign of a nitrogen deficiency, as this element is prominent in photosynthesis as well as growth. But stunted growth could also arise from a herbicide, toxicity in the soil (eg aluminium), the ‘wrong’ soil pH, a bacterial or fungal disease preventing transportation of nutrients in general, or simply some other nutrient deficiency(ies) altogether.
While these things should always be considered, and barring a soil and/or leaf analysis which would confirm nitrogen levels definitively, stunted, starved growth is still a common enough sign of a nitrogen deficiency to suspect one. Another strong sign is the presence of yellowing leaves, but even here other factors must still be considered, as yellowing leaves can also be caused by other deficiencies, soil pH, diseases, or simply too little or too much watering!
Nitrogen-deprived leaves yellow as they suffer from chlorosis, or the insufficient production of chlorophylls. This leads to a collapse of chloroplasts and lack of development of new ones. Chlorophylls are green, thus a lack of these reveal the yellow pigments (the carotenoids) also in a leaf. As nitrogen is a major component of chlorophylls, and chloroplasts are in every leaf cell, nitrogen deficiency usually shows as a uniform chlorosis across the entire leaf, which turns yellow or yellow-white. The leaf may further turn brown, die and fall off.
Other deficiencies, such as in potassium (K), magnesium (Mg), iron (Fe), calcium (Ca), and sulfur (S) can also produce yellow leaves, but there are two general differences that help distinguish these from a nitrogen deficiency.
The first difference is that potassium and magnesium deficiencies are both marked by chlorotic and necrotic (localised, dead) spots in older leaves, but appear at a very early stage. Chlorosis induced by a nitrogen deficiency is more even across the leaf, and necrosis of the leaf, or part of the leaf, only occurs at a very late stage of the deficiency.
The second difference is that while iron, calcium and sulfur deficiencies also result in yellow and pale leaves, the symptoms first appear in the younger leaves. A nitrogen deficiency begins in the older leaves at the bottom of a plant. Nitrogen is highly mobile in plants, thus that obtained from the degrading chloroplasts in lower leaves can be relocated to newer growing leaves higher up the plant which remain healthy and green. Unless, of course, the deficiency is so bad the entire plant succumbs.
Nitrogen Toxicity Symptoms
All fertilisers contain good amounts of nitrogen, as it is such a well-known and crucial macronutrient. Following the manufacturer’s directions is always recommended, for the same reason you should follow instructions on prescription medication — to avoid an overdose and minimise side effects. It can be very tempting to think if some is good then more is better, and over-apply. Often in the case of fertilisers this leads to nothing more than a waste of money and product, as any excess nitrogen compounds are either taken up by microbes in the nitrogen cycle (if applied as ammonium) or simply leached away before the plant can use them (if applied as nitrate).
It is still possible to create a nitrogen toxicity however, especially if applying large amounts of ‘hot’ manures that haven’t been aged or composted first. Nitrogen toxicity can also be a problem in hydroponics systems if incorrect fertiliser mixes are applied and/or the pH of the solution wasn’t monitored and adjusted.
High levels of nitrogen can led to ‘nitrogen burning’. This is when nitrogen salts (specifically ammonium salts) are so concentrated around the roots that they draw water out of the root cells via osmosis [a phenomenon whereby water flows from an area of higher purity (here, the root cell) into a region of lower purity (the soil) until equilibrium is established. This is also why you wrinkle when in salt water long enough!]. This creates a flow-on effect, whereby water enters the now dehydrated root cells from surrounding cells, and so on. Eventually water is drawn from the cells on leaf edges, which are the ‘end of the line’ with no further cells to draw water from. These edge cells, drained and dehydrated, will die and collectively create yellow or brown edges that make the affected leaves appear ‘burnt’. Flushing the soil with copious watering can correct this, but if salt concentrations were so high that root cells died then the plant is not likely to survive.
Another sign of nitrogen toxicity is overly-rapid, jungle-like growth, as the excess nitrogen finds a home in increased chlorophyll production and cellular division. Still another, related, sign of toxicity is a very noticeable darkening of the leaves from all the extra chlorophyll in all the extra leaf cells. These cells may be smaller and more packed in the leaf because of the accelerated growth, which increases the chlorophyll density compared to a similar area of a normal leaf.
Excess nitrogen fuels growth, and a nitrogen-rich plant will look lush and healthy on the outside, almost succulent. But this is at the expense of root and flower development, as all that nitrogen has to go somewhere first, which is into the stems and leaves which use it, and not the roots and flowers which don’t. Worse, excess nitrogen prevents potassium uptake, further exacerbating flowering and fruiting problems.
In short, nitrogen-rich plants tend to be top-heavy and unstable from the excess growth, with stunted roots and an inability to reproduce. The additional stem and leaf tissue produced also holds more water than usual, which makes them more attractive to mites and other pests.
If you’ve always known that nitrogen is ‘important’, but wanted more detail other than ‘for growth’, I do hope this post has helped! Having a deeper understanding of what makes nitrogen an essential macronutrient can only help understand the interactions of other nutrients too. And these we will cover one by one, with potassium the next one in line.