Organismal Biology · Unit 6: How plants work

Soil, Nutrients and Partners

A plant makes every organic molecule it contains from carbon dioxide, water and a short list of mineral elements, so what must it get from the soil, and how does it get it? This lesson lists the 17 elements conventionally essential to vascular plants, reads a sick leaf by where the symptoms appear first, follows water and ions into the root past the endodermis, and compares plants that take nitrogen and phosphorus from bacteria, fungi, insects or other plants. Afterwards you can design a test of essentiality, diagnose a deficiency from leaf age, and calculate how much surface root hairs and fungal hyphae add to a root.

Watch first Peas Borrow Nitrogen From Bacteria · 2:47

Peas grown in sterilised sand, given a little soil extract and watered with a solution that held no nitrogen, ended up with many times more nitrogen than their seeds contained. Oats in the next pot starved. Nitrogen gas makes up most of the air around both plants, so why could one use it and the other not? Answering that takes you through what a plant takes from the soil, how a root lets it in, and the partners some plants rely on.

What a plant must get from the soil

Start with a contrast to animals. You must eat certain amino acids and vitamins because your cells cannot make them, as digestive systems explains. A green plant builds every organic molecule it contains, every amino acid, lipid and nucleotide, from carbon dioxide, water and a short list of mineral elements. Photosynthesis fixes the carbon in the leaf; the chemistry of that belongs to the Calvin cycle. What the plant cannot make is an element. It has to take each one in.

An element is essential if, without it, a plant cannot complete its life cycle from seed to seed. Daniel Arnon and Perry Stout added two more conditions in 1939: no other element can stand in for it, and it acts directly in the plant rather than by changing the soil or its microbes.

The conventional list for vascular plants has 17 essential elements:

  • From air and water: carbon, hydrogen and oxygen.
  • Macronutrients (required in larger amounts): nitrogen, phosphorus, potassium, calcium, magnesium and sulfur.
  • Micronutrients (required in trace amounts): chlorine, boron, iron, manganese, copper, zinc, nickel and molybdenum.

Some tables list 20. The extra elements are beneficial: they improve growth in some species but are not universal requirements. Sodium helps some plants with C4 or CAM photosynthesis, silicon strengthens grasses such as rice, and cobalt is used by the nitrogen-fixing bacteria in legume nodules.

The list was built in water culture. Dennis Hoagland and Arnon published a standard nutrient solution in 1938, and leaving one element out of it, then putting it back, is still the basic test.

Reading a sick leaf

A deficiency shows on the leaves, and where it shows first is a clue. The key is mobility: whether the plant can move an element out of old tissue and through the phloem to growing tissue.

AI-generated illustration: two matching green plants side by side. On the left, the three oldest lower leaves are yellow, the two young top leaves are green, and a gold arrow runs up the stem to the tip. On the right, the two young top leaves are yellow and the old leaves are green.
Nitrogen, phosphorus, potassium and magnesium are mobile, so a shortage shows first in old, lower leaves; iron, calcium and, in most species, boron stay where they were deposited, so a shortage shows first in young leaves. Treat these as examples, not a key for every species.
  • Mobile elements (nitrogen, phosphorus, potassium, magnesium) are withdrawn from old leaves when supply runs short. Symptoms appear first in old, lower leaves.
  • Immobile elements (iron and calcium, and boron in most species) stay where they were deposited. New leaves get only what arrives from the roots, so symptoms appear first in young leaves and growing tips.

Here chlorosis means yellowing from lost chlorophyll, and necrosis means patches of dead tissue.

A study of Japanese mint (Mentha arvensis), grown in greenhouse hydroponics with one nutrient left out of Hoagland’s solution at a time, shows the pattern. Without nitrogen, the whole blade of old leaves yellowed first, with symptoms first seen 15 days after transplanting. Without iron, young leaves yellowed. Without potassium, old leaves developed yellow spots. Without phosphorus, blades turned dark green with purple margins. In sweetgum, magnesium deficiency can yellow the tissue between the veins while the veins stay green.

Treat these as examples, not a key for every species. Different deficiencies can look alike, and drought, disease or cold can mimic them. A symptom is a hypothesis. Tissue analysis, measuring the elements in the leaf, tests it, and add-back, supplying the suspected element and watching new growth recover, confirms it.

Into the root: hairs, two routes and a gatekeeper

Most uptake happens near the root tip, where root hairs, tubular outgrowths of single epidermal cells, push into the spaces between soil particles and enlarge the absorbing surface.

Worked problem: how much surface do hairs and hyphae add? These are illustrative numbers, not measurements from one species. Treat every structure as a cylinder and ignore the ends.

side area of a cylinder = pi x d x L surface per volume of a cylinder = 4 / d

  1. The root. A 10 mm segment, 0.5 mm in diameter: pi x 0.5 mm x 10 mm = 15.7 mm2.
  2. The hairs. Suppose 1,000 hairs on that segment, each 0.5 mm long and 0.010 mm wide. One hair: pi x 0.010 mm x 0.5 mm = 0.0157 mm2. All of them: 1,000 x 0.0157 = 15.7 mm2. The hairs double the surface, to 31.4 mm2.
  3. The fungus. Suppose 1 m (1,000 mm) of mycorrhizal hyphae, each 0.004 mm wide, attached to the segment: pi x 0.004 mm x 1,000 mm = 12.6 mm2. The total is now 15.7 + 15.7 + 12.6 = 44.0 mm2.
  4. Surface per material. With 4 / d, the root gives 4 / 0.5 = 8 per mm, a hair 4 / 0.010 = 400 per mm and a hypha 4 / 0.004 = 1,000 per mm. Check by volume: the hyphae occupy pi x (0.002 mm)2 x 1,000 mm = 0.013 mm3, against 2.0 mm3 for the root segment. They add more than three quarters of the root’s own surface for under one per cent of its volume.

Surface matters most for ions that move slowly through soil. Phosphate diffuses so slowly that a root soon empties the soil right around it, and thin hyphae reach past that emptied zone. Hairs help with water too, but not equally everywhere: in barley, root hairs aided water extraction by rapidly transpiring plants in drying soil, while a hairless maize mutant took up water no differently in sand or loam. (Moving water and sugar in plants covers water potential and the pull of transpiration.)

Root hairs and fungal hyphae — how much surface do they add?⚙ original · interactive
View:

In this sketch: illustrative numbers, not a measured species; every structure is a cylinder; ends ignored; not to scale; drawn lines are a sample, not a count.

Side area of a cylinder = π × d × L, and surface per volume of a cylinder = 4 / d, so the thinner the cylinder, the more surface per unit of material.

Inside the root, water and dissolved ions cross the cortex by two routes. The apoplast is the continuous network of cell walls and spaces outside the membranes. The symplast is the cytoplasm of cells joined by plasmodesmata, channels through the walls. Both routes reach the endodermis, the innermost cortical layer around the central cylinder. In the walls between endodermal cells runs the Casparian strip, a band that blocks the wall route. In young Arabidopsis roots that band is lignin, not suberin as older textbooks say; suberin is laid down later. Past the strip, anything heading for the xylem has to cross a living membrane, so the endodermis acts as a gatekeeper on what enters.

Taking up many nutrient ions takes energy, because they often move against their gradients. A proton pump, an ATP-driven H+-ATPase of the P type in the plasma membrane, moves protons out of root cells. Transporters then let a proton flow back in with nitrate or another ion, cotransport. In Arabidopsis the NRT1.1 nitrate transporter works this way. How such transporters work is in membrane transport.

Borrowing nitrogen and phosphorus: nodules and mycorrhizae

Back to the peas. At the Bernburg experiment station, Hermann Hellriegel and Hermann Wilfarth grew legumes, including peas, and cereals, including oats, in sterilised sand with a nitrogen-free nutrient solution, and published the work in 1888. If every plant relied on nitrogen compounds in soil, none should end with more nitrogen than its seed held. The cereals grew only as far as the nitrate they were given allowed. Peas given a little extract of field soil formed nodules, swellings on the roots, and gained much nitrogen from the air. Without the extract, or with extract that had been heated, they formed no nodules and did not. A living agent from soil, tied to the nodules, was required. The experiment did not identify the agent; in the same year Martinus Beijerinck reported isolating bacteria from nodules.

AI-generated illustration: three identical glass pots of pale sand, each with one pea plant. The left pot, given live soil extract, has a tall plant with round nodules on its roots. The middle pot, with no extract, and the right pot, with heated extract, have small plants and smooth roots. An inset shows a pea root with round nodules.
Hellriegel and Wilfarth grew peas in sterilised sand with a nitrogen-free solution. Only peas given live soil extract formed nodules and gained nitrogen from the air; without the extract, or with extract that had been heated, they did not.

Those bacteria are rhizobia. They enter the root, and inside nodule cells they become bacteroids whose enzyme, nitrogenase, reduces nitrogen gas to ammonia. The root makes no nitrogenase. In return the plant supplies carbon: sucrose from the leaves is converted to malate, which fuels the bacteroids. Nitrogenase is damaged by oxygen, yet the bacteroids respire. A plant protein, leghemoglobin, binds oxygen and buffers it at a low, steady level. It does not exclude oxygen. In Lotus japonicus, Ott and colleagues (2005) silenced leghemoglobin: free oxygen in nodules rose, fixation stopped, and the plants grew normally only when given mineral nitrogen. Oats and barley have no nodules and depend on nitrate and ammonium in the soil. The ecosystem side of fixation is in nutrient cycling.

Phosphorus is borrowed from fungi. A mycorrhiza is an association of a root with a fungus (fungal hyphae appear in microbes, protists and fungi).

  • Arbuscular mycorrhizae form in most land plants. Hyphae enter cortex cells and branch into arbuscules, tree-like structures where nutrients are released. In Lotus japonicus with the fungus Rhizophagus irregularis, the fungus delivers minerals taken from soil, especially phosphate. Keymer and colleagues (2017) showed with isotope labelling and plant mutants that the plant pays in lipids as well as sugars.
  • Ectomycorrhizae form on trees such as pines and oaks. The fungus wraps the root tip in a sheath and grows between cortex cells without entering them.

Partners differ in quality, and hosts can respond to that, as mutualism, parasitism and coevolution explains.

Plants that eat animals and plants that tap plants

The purple pitcher plant, Sarracenia purpurea, grows in nitrogen-poor bogs. It photosynthesizes like any green plant, and its flat leaves, phyllodia, photosynthesize more efficiently than its pitchers. Insects drown in rainwater held in the pitchers, where bacteria, protists and larvae break them down, releasing mineral nitrogen and also competing with the plant for it. Karagatzides, Butler and Ellison (2009) added labelled amino acids to pitchers in Ontario and Massachusetts and found data consistent with direct amino-acid uptake by the plant, clearest for phenylalanine.

Dodder (Cuscuta) takes a different route. This twining stem parasite forms haustoria, organs that grow into the host stem and connect to its xylem and phloem, drawing water, nutrients and sugars.

A pea borrows from bacteria, a pine from fungi, a pitcher plant from insects and a food web, and dodder from another plant. In those pots, oats had only the nitrate their solution held.

Design problem

Brown, Welch and Cary (Plant Physiology, 1987) asked whether nickel is essential for barley (Hordeum vulgare, cultivar Onda). Nickel is needed in such small amounts that contamination from salts, water and the seed itself can hide a requirement. Design the test.

One way to do it

Grow barley in solution culture made with purified salts and clean water, so the solution is depleted of nickel. Give one group no added nickel and a second group the same solution plus nickel, and keep a third group of deficient plants for later add-back. Run the experiment for the whole life cycle and into the next generation, because a seed carries nickel from its mother, and a first-generation plant may live on that store. Measure grain nickel and test whether the grain germinates. In the published experiment, adding nickel completely relieved the deficiency symptoms in the mother plants, and grain with less than 30 ng of nickel per gram of dry weight was not viable. Failure without nickel and rescue with it meet the Arnon and Stout criterion of a life cycle that cannot be completed without the element. The limits: this was one cereal in one preparation, so it does not give a threshold for all plants or any fertiliser rate.

How plants sense and respond to what they find, through hormones, comes next in plant signals.

How we measure it

Solution culture with omission and add-back

Grow plants in a complete nutrient solution made from purified salts, and in matching solutions each lacking one element, then add the element back to some deficient plants. A symptom that appears on omission and disappears on add-back ties the symptom to that element in that species.

Tissue elemental analysis

Dry and dissolve leaf or grain tissue and measure its elements, today often by inductively coupled plasma mass spectrometry (ICP-MS). It tests a diagnosis made from symptoms, since different deficiencies can look alike.

Stable-isotope pulse-chase

Supply a compound labelled with a heavy isotope, such as nitrogen-15 in amino acids, and measure where the label turns up over the following hours or days. It shows which route a nutrient took into a plant or between partners.

Tracer dye exclusion at the endodermis

Bathe roots in a dye such as propidium iodide that travels in cell walls but does not cross intact membranes, and look under the microscope for whether it reaches the central cylinder. An intact Casparian strip stops it at the endodermis.

Finish line

Test yourself

8 questions

Practice and MCAT-style, with explained answers.

Next · Lesson 25

Plant Hormones and Responses

Light an oat seedling from one side and it bends toward the lamp. The tip senses the light, yet the bend forms lower down. What told it?

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← Lesson 23 · Moving Water and Sugar in Plants

Hermann Hellriegel and Hermann Wilfarth

Hermann Hellriegel and Hermann Wilfarth

Grew peas and other legumes beside oats in nitrogen-free sand culture, and showed that legumes gained nitrogen from the air only when a living agent from soil was present and root nodules formed, while the cereals depended on nitrogen compounds supplied to the roots.

By the 1880s agricultural chemists knew that clover, peas and beans left a field richer in nitrogen, and that cereals did not, but they disagreed about why. At the agricultural experiment station in Bernburg, in Anhalt, Hellriegel and Wilfarth tested the question in pots. They grew legumes, including peas, and cereals, including oats, in washed and sterilised sand watered with a nutrient solution that held every mineral element but no nitrogen. The cereals stayed small unless nitrate was added, and their growth followed the nitrate they were given. Peas without the extract behaved like the cereals and grew only as far as their nitrogen supply allowed. Peas given a little extract shaken from field soil formed nodules on their roots, grew well, and ended up with far more nitrogen than their seeds had held. When the extract had been heated first, peas formed no nodules and gained no nitrogen. The experiment showed that legume nitrogen gain depends on a living agent in soil, tied to the nodules, and it set the problem that later microbiologists solved by isolating nodule bacteria.

✓ verbatim Hellriegel H, Wilfarth H, Untersuchungen über die Stickstoffnahrung der Gramineen und Leguminosen (Berlin, 1888), issued as a supplement to the Zeitschrift des Vereins für die Rübenzucker-Industrie des Deutschen Reichs.
Dennis R. Hoagland

Dennis R. Hoagland

With Daniel Arnon, wrote the standard recipe and method for growing plants in water culture, the nutrient solution still called Hoagland's solution, which made controlled omission experiments routine.

Hoagland worked at the University of California for most of his career, on how roots take up ions from soil and from solution. His academy memoir, written by Walter Kelley, places one early project during American participation in the First World War: a study of the giant kelp off California as a possible source of potassium fertiliser, at a time when much of the world's potash came from German mines. His laboratory then turned to the plant itself, growing roots in solutions whose composition could be set and measured, and asking how much of each ion they took in. A water culture is a clean experiment only if the solution is reproducible, and in 1938 Hoagland and his student Daniel Arnon published a circular for the state agricultural experiment station that gave a recipe and the practical steps. Versions of that solution are still the default in plant laboratories, including the Japanese mint omission experiment described in this lesson. A shared recipe let laboratories compare their deficiency results directly.

✓ verbatim Hoagland DR, Arnon DI, The water-culture method for growing plants without soil, California Agricultural Experiment Station Circular 347 (1938; revised 1950); Kelley WP, Dennis Robert Hoagland, National Academy of Sciences Biographical Memoirs (1956).
Daniel I. Arnon

Daniel I. Arnon

With Perry Stout, stated in 1939 the criteria by which an element counts as essential to a plant, the test that the nickel experiment on barley later met.

Arnon trained in Hoagland's laboratory at Berkeley, where his academy memoir records that he earned his doctorate in 1936. Water culture raised a practical problem. Salts and glassware carry traces of many elements, so a plant that grows without an added element may simply be living on contamination, and a plant that grows better with an element may be using it without requiring it. Arnon and Perry Stout set out what a claim of essentiality has to show: without the element the plant cannot complete its life cycle; no other element can take its place; and its effect is direct, inside the plant, rather than through some change in the solution or the microbes around the root. Those criteria are still the working definition. The memoir also records that from 1943 to 1946 Arnon directed a project that grew food plants by nutrient culture on Ascension Island. His later work turned to photosynthesis, which the Biochemistry course covers.

✓ verbatim Arnon DI, Stout PR, The essentiality of certain elements in minute quantity for plants with special reference to copper, Plant Physiology 14:371-375 (1939); Buchanan BB, Daniel I. Arnon, National Academy of Sciences Biographical Memoirs 80 (2001).
Test yourself
Question 1 of 8 Score 0 / 0

Which group lists only mineral elements that are conventionally essential micronutrients for vascular plants?
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Every structure, slide, simulation, and clip on this page is listed below with the source it came from. None of the 3D structures is drawn by hand or by AI: each one loads by accession ID from RCSB PDB or PubChem. This panel is generated from the lesson's own data file, so what it lists is what the page loads.

Simulations

  • Hairs, hyphae and surface · Original interactive — Biochemistrypedia (Deppmann Lab).

Scientist profiles & quotes

  • Hermann Hellriegel and Hermann Wilfarth — Hellriegel H, Wilfarth H, Untersuchungen über die Stickstoffnahrung der Gramineen und Leguminosen (Berlin, 1888), issued as a supplement to the Zeitschrift des Vereins für die Rübenzucker-Industrie des Deutschen Reichs.
  • Dennis R. Hoagland — Hoagland DR, Arnon DI, The water-culture method for growing plants without soil, California Agricultural Experiment Station Circular 347 (1938; revised 1950); Kelley WP, Dennis Robert Hoagland, National Academy of Sciences Biographical Memoirs (1956).
  • Daniel I. Arnon — Arnon DI, Stout PR, The essentiality of certain elements in minute quantity for plants with special reference to copper, Plant Physiology 14:371-375 (1939); Buchanan BB, Daniel I. Arnon, National Academy of Sciences Biographical Memoirs 80 (2001).

Quotes are verbatim from the cited source. Profile text is original to this site and was checked against the sources cited.

Animated explainer

Peas Borrow Nitrogen From Bacteria · narration: an AI narrator voice (Gemini, Charon) reading narration written from this lesson's text · animation: AI-generated in code (Manim) by Claude, a schematic with no drawn molecular structures, plots computed from their equations · captions from the narration script.

Images & figures

2 illustrations in this lesson are AI-generated: drawn by an image model from a written spec, then checked by a separate AI judge against the spec and the lesson text. None shows a chemical structure or data.

  • two matching green plants side by side. On the left, the three oldest lower leaves are yellow, the two young top leaves are green, and a gold arrow runs up the stem to the tip. On the right, the two young top leaves are yellow and the old leaves are green.
  • three identical glass pots of pale sand, each with one pea plant. The left pot, given live soil extract, has a tall plant with round nodules on its roots. The middle pot, with no extract, and the right pot, with heated extract, have small plants and smooth roots. An inset shows a pea root with round nodules.

Every 3D structure is rendered live from an accession ID, and every plot is drawn from its equation in the browser.

integrity Machines check the mechanics. The build confirms that every local file exists, that every question's answer key points at a real choice, and that any AI-generated scientific figure names the person who checked it; a weekly job re-resolves every accession ID against its database. Questions are original; MCAT-style items are written for this site and are not real AAMC questions. Banned sources (the Tymoczko textbook, publisher decks, copyrighted figures) are not used.

Like I'm five

A plant makes its own food from air, water and sunlight, but it also has to pick up tiny amounts of minerals from the soil, such as nitrogen, phosphorus and iron. Its roots have little hairs that soak these up. Some plants get help: beans keep tiny bacteria in bumps on their roots that pull nitrogen out of the air, and many plants share sugar with fungi that bring back food from farther away.
High school

Plants require 17 elements to complete their life cycle. Carbon, hydrogen and oxygen come from air and water; the other 14 are minerals taken from the soil. Roots take them in through a large surface, enlarged by root hairs, and a layer called the endodermis acts as a checkpoint, so that ions have to pass through living cells before reaching the xylem. When a nutrient runs short, leaves show it: old leaves first if the plant can move the nutrient to new growth, young leaves first if it cannot. Legumes such as peas get nitrogen from bacteria in root nodules, most land plants trade sugar with mycorrhizal fungi for phosphorus and other minerals, pitcher plants digest insects, and dodder taps another plant's plumbing.
College

An element is essential if a plant cannot complete its life cycle without it, no other element substitutes, and its role is direct (Arnon and Stout, 1939). The conventional list for vascular plants is 17: carbon, hydrogen and oxygen; the macronutrients nitrogen, phosphorus, potassium, calcium, magnesium and sulfur; and the micronutrients chlorine, boron, iron, manganese, copper, zinc, nickel and molybdenum. Phloem-mobile nutrients (nitrogen, phosphorus, potassium, magnesium) show deficiency in old leaves first; immobile ones (iron, calcium, and boron in most species) in young leaves. Water and ions cross the cortex in the apoplast and the symplast, but the Casparian strip in endodermal walls blocks the apoplast, forcing solutes across a membrane, where a P-type proton pump builds the gradient that drives cotransporters. Rhizobial bacteroids in legume nodules fix nitrogen with nitrogenase, with leghemoglobin buffering oxygen; arbuscular mycorrhizal fungi deliver phosphate and other minerals and, in Lotus japonicus, receive lipids as well as sugars.
Graduate

Uptake of a slowly diffusing ion such as phosphate from a low-supply soil can be limited by transport to the surface more than by the transporters, so absorbing surface and reach matter more than root mass. For a cylinder, surface per volume is 4/d: a 0.5 mm root gives 8 per mm, a 0.010 mm root hair 400 per mm and a 0.004 mm hypha 1,000 per mm, so a fungus builds more surface per unit of material and extends beyond the depletion zone that forms around a root. The plant pays in fixed carbon, and in Lotus japonicus with Rhizophagus irregularis part of that payment is lipid. Nodulated legumes pay too, with photosynthate converted to malate for the bacteroids. The same logic does not transfer simply from one species to another: root hairs aided water extraction by rapidly transpiring barley in drying soil, but a hairless maize mutant showed no difference in sand or loam. An open question is how hosts and partners settle the rate of exchange in mixed soil communities, where one root meets many fungal and bacterial partners of differing quality.
Growing vegetables on a volcanic island

Ascension Island, in the middle of the South Atlantic, served as an airfield during the Second World War, and fresh food had to be shipped a long way to reach it. According to Bob Buchanan's academy memoir, Daniel Arnon spent 1943 to 1946 in charge of a project there that grew food plants by nutrient culture, with roots fed a prepared solution instead of soil. The laboratory method of Hoagland and Arnon, made for controlled experiments, became a way of feeding people where the soil could not.

— Buchanan BB, Daniel I. Arnon 1910-1994, National Academy of Sciences Biographical Memoirs 80 (2001).
A pitcher with a food web inside

The pitchers of Sarracenia purpurea fill with rainwater, and insects that fall in are broken down by a community of bacteria, protists and insect larvae living in the fluid. That community releases mineral nitrogen from prey, but it also takes nitrogen for itself and so competes with the plant. Tracer work in Ontario and Massachusetts bogs was consistent with direct uptake of at least one amino acid by the pitcher as well. The plant photosynthesizes throughout, and its flat leaves, phyllodia, do so more efficiently than its pitchers.

— Karagatzides JD, Butler JL, Ellison AM, PLoS ONE 4:e6164 (2009); Ellison AM, Gotelli NJ, PNAS 99:4409-4412 (2002).

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