Nutrient Acquisition by Plants

Learning Objectives

  1. Describe the formation and structure of soil
  2. Explain the role of root hairs, proton pumps, ion channels, and co-transporters in acquisition of water, ions, and minerals by plants
  3. Explain why and how soil composition and texture influences acquisition of water, ions, and minerals by plants
  4. Compare and contrast the roles of rhyzobia bacteria and mycorrhizal fungi in nutrient acquisition by plant roots

The information below was adapted from OpenStax Biology 31.2

Soil Composition and Texture

Soil is formed from weathering of rock by mechanical (physical), chemical, and biological processes. Soils differ dramatically in different regions, but all consists of living and nonliving components:

  • Humus: organic matter (living and dead), including plant roots, prokaryotic and eukaryotic microorganisms, decomposing plants/animals; comprises about 5% of soil volume
  • Rock fragments and other inorganic mineral matter from rock, slowly broken down into smaller particles that vary in size; comprises about 40 to 45% of soil volume
  • Water and gasses (air) which are dissolved in the soil particles; comprise about 50 % of soil volume

The amount of each of the major components of soil depends on the amount of vegetation, soil compaction, and water present in the soil. A good healthy soil has sufficient air, water, minerals, and organic material to promote and sustain plant life.

The typical approximate composition of soil. Forty-five percent is inorganic mineral matter, 25 percent is water, 25 percent is air, and 5 percent is organic matter, including microorganisms and macroorganisms. Image credit: OpenStax Biology.


Soil texture is determined by the proportions of differently-sized particles in the soil, which affects both the ability of plant roots to penetrate the soil, and the ability of the soil to hold water. Soils are categorized by texture as follows:

  • Gravel: particles larger than 2.0 mm in diameter
  • Sand: particles between 0.02 to 2 mm in diameter
  • Silt: particles between 0.002 and 0.02 mm
  • Clay: particles less than 0.002 mm in diameter
  • Loam: soil composed of a a mixture of sand, silt, and humus

Soil Formation

Five main factors dictate soil formation: parent material, climate, topography, biological factors, and time.

  • Parent Material: The organic and inorganic material in which soils form is the parent material, such as bedrock, sand, glacial drift, river sediment.
  • Climate: Temperature, moisture, and wind cause different patterns of weathering and therefore affect soil characteristics. The presence of moisture and nutrients from weathering will also promote biological activity: a key component of a quality soil.
  • Topography: Regional surface features (familiarly called “the lay of the land”) can have a major influence on the characteristics and fertility of a soil. Topography affects water runoff, which strips away parent material and affects plant growth. Steeps soils are more prone to erosion and may be thinner than soils that are relatively flat or level.
  • Biological factors: Animals and microorganisms can produce pores and crevices, and plant roots can penetrate into crevices to produce more fragmentation. Plant secretions promote the development of microorganisms around the root, in an area known as the rhizosphere. Additionally, leaves and other material that fall from plants decompose and contribute to soil composition.
  • Time: Time is an important factor in soil formation because soils develop over long periods. Soil formation is a dynamic process. Materials are deposited over time, decompose, and transform into other materials that can be used by living organisms or deposited onto the surface of the soil. Depending on the climate, it is estimated to take between 200 to 1000 years to create 1 inch of soil.

Once they are formed, soils are named and classified based on their “horizons,” or layers. Soil typically has four types of horizons, or layers:

  1. O horizon: freshly decomposing organic matter (humus)
  2. A horizon: topsoil that is rich in organic matter mixed with inorganic material; the most important soil layer for plant growth; usually only 2-3 inches deep
  3. B horizon: subsoil comprised of a dense layer of of fine material which has shifted downard
  4. C horizon: soil base comprised of parent material plus organic and inorganic material; beneath the C horizon lies the bedrock

The O horizon is a rich, deep brown color. From two to ten inches is the A horizon. This layer is slightly lighter in color than the O horizon, and extensive root systems are visible. From ten to thirty inches is the B horizon. The B horizon is reddish brown. Longer roots extend to the bottom of this layer. The C horizon extends from 30 to 48 inches. This layer is rocky and devoid of roots. Image credit: OpenStax Biology.

Some soils may have additional layers, or lack one of these layers. The thickness of the layers is also variable, and depends on the factors that influence soil formation. In general, immature soils may have O, A, and C horizons, whereas mature soils may display all of these, plus additional layers.

With the amount of time it takes to form soil, what happens when we lose soil to erosion and other processes? This video describes the implications for this phenomenon which can ultimately lead to desertification:


Uptake of Mineral Nutrients from the Soil

The information below was adapted from OpenStax Biology 30.3,

Most plants are autotrophic, and use photosynthesis to make their own food from inorganic raw materials, such as carbon dioxide and water. (Some plants, are heterotrophic: they are totally parasitic and lacking in chlorophyll. Heterotrophic plants are unable to synthesize organic carbon and draw all of their nutrients from a host plant.)

This video reviews basic concepts about photosynthesis. In the left panel, click each tab to select a topic for review.

Even though most plants are autotrophs and can generate their own sugars from carbon dioxide and water, they still require certain ions and minerals from the soil. How to plants acquire micronutrients from the soil?  This process is mediated by root hairs, which are extensions of the root epidermal tissue that increase the surface area of the root, greatly contributing to the absorption of water and minerals.

Root hairs absorb ions that are dissolved in the water in soil. However, not all ions are equally available in soil water, depending on the properties of the soil.  Clay is negatively charged, and thus any positive ions (cations) present in clay-rich soils will remain tightly bound to the clay particles. This tight association with clay particles prevents the cations from being washed away by heavy rains, but it also prevents the cations from being easily absorbed by plant root hairs. In contrast, anions are easily dissolved in soil water and thus readily accessible to plant root hairs; however, they are also very easily washed away by rainwater. In his way, the presence of clay particles present a trade-off for plants: they prevent leaching of cations from the soil by rainwater, but they also prevent absorption of the cations by the plant.

How do plants overcome these issues? The epidermal tissue of root hairs is lined by proton pumps (H+ ATPases), which use ATP as an energy source to pump protons out of the cells and into the soils, against their electrochemical gradient. These proton pumps create a strong electrochemical gradient with a high concentration of protons and a strong positive charge outside of the cell, and a low concentration of protons and relatively negative charge inside of the cell. These protons pumped into the soil by the proton pumps results in two outcomes:

  1. Protons bind to the negatively-charged clay particles, releasing the cations from the clay in a process called cation exchange. The cations then diffuse down their electrochemical gradient into the root hairs. (The soil environment is highly positively charged, so it is favorable for cations to move into the root hairs).
  2. The high concentration of protons in the soil creates a strong electrochemical gradient that favors transport of protons back into the root hairs. Plants use co-transport of protons down their concentration gradient as the energy source to move anions against their electrical gradient into the root hairs. (The soil environment is highly positively charged, so it is unfavorable for anions to leave the soil, but highly favorable for protons to leave the soil).

Due to the influence of pH and clay on ion retention as well as other parameters, the composition and texture of soil greatly influences the ability of roots to penetrate the soil, as well as the availability of water, nutrients, and oxygen:

Composition Water availability Nutrient availability Oxygen availability Root penetration ability
Sand Low: water drains out Low: poor capacity for cation exchange; anions leach out High: many air-containing spaces High: large particles do not pack tightly
Clay High: water clings to charged surface of clay particles High: large capacity for cation exchange; anions remain in solution Low: few air-containing spaces Low: small particles pack tightly
Organic matter High: water clings to charged surface of clay particles High: ready source of nutrients, large capacity for cation exchange; anions remain in solution High: many air-containing spaces High: large particles do not pack tightly


Watch the videos below for discussion of these interactions, including the importance of pH and clay in soils and the process of cation exchange utilized by plants to acquire nutrients from clay-rich soils.



The video below reviews the basic principles of active and passive transport (start at 1 min 7 sec and watch through 5 min 14 sec)  These processes will be discussed in more specific contexts of root transport in class.

Plant relationships with other organisms

While plants have ready access to carbon (carbon dioxide) and water (except in dry climates or during drought), they msut extract minerals and ions from the soil. Often nitrogen is most limiting for plant growth; while it comprises approximately 80% of the atmosphere, gaseous nitrogen is chemically stable and not biologically available to plants. Many plants have evolved mutualistic relationships with microorganisms, such as specific species of bacteria and fungi, to enhance their ability to acquire nitrogen and other nutrients from the soil. This relationship improves the nutrition of both the plant and the microbe.

The Nitrogen Cycle

Though the atmosphere is 80% nitrogen, nitrogen in its gaseous form is unavailable to most organisms. Only a few species of bacteria are able to “fix” nitrogen, and all biologically-available nitrogen comes from the activities of these bacteria. Plants are able to utilize nitrogen from nitrogen-fixing bacteria or from nitrogen releaed by decomposers such as fungi. By Cicle_del_nitrogen_de.svg: *Cicle_del_nitrogen_ca.svg: Johann Dréo (User:Nojhan), traduction de Joanjoc d’après Image:Cycle azote fr.svg.derivative work: Burkhard (talk)Nitrogen_Cycle.jpg: Environmental Protection Agencyderivative work: Raeky (talk) – Cicle_del_nitrogen_de.svgNitrogen_Cycle.jpg, CC BY-SA 3.0,

Rhizobia and legumes: mutualistic relationship between bacteria and roots

Nitrogen is an important macronutrient because it is part of nucleic acids and proteins. Atmospheric nitrogen, which is the diatomic molecule N2, or dinitrogen, is the largest pool of nitrogen in terrestrial ecosystems. However, plants cannot take advantage of this nitrogen because they do not have the necessary enzymes to convert it into biologically useful forms. However, nitrogen can be “fixed”which means that it can be converted to ammonia (NH3) through biological, physical, or chemical processes. Biological nitrogen fixation (BNF) is the conversion of atmospheric nitrogen (N2) into ammonia (NH3), exclusively carried out by prokaryotes such as soil bacteria or cyanobacteria. Biological processes contribute 65 percent of the nitrogen used in agriculture.

The most important source of BNF is the symbiotic and mutualistic interaction between soil bacteria and legume plants, including many crops important to humans. The NH3 resulting from fixation can be transported into plant tissue and incorporated into amino acids, which are then made into plant proteins. Some legume seeds, such as soybeans and peanuts, contain high levels of protein, and serve among the most important agricultural sources of protein in the world.

Specific soil bacteria called rhizobia can symbiotically interact with legume roots to form specialized structures called nodules, in which nitrogen fixation takes place. This process entails the reduction of atmospheric nitrogen to ammonia, by means of the enzyme nitrogenase. Through symbiotic nitrogen fixation, the plant benefits from using an endless source of nitrogen from the atmosphere. The process simultaneously contributes to soil fertility because the plant root system leaves behind some of the biologically available nitrogen. As in any symbiotic mutualism, both organisms benefit from the interaction: the plant obtains ammonia, and bacteria obtain carbon compounds generated through photosynthesis, as well as a protected niche in which to grow.  Importantly, the nitrogenase enzyme is inactivated in the presence of oxygen, and thus the root nodules help maintain a low concentration of oxygen to “protect” the nitrogenase within the rhizobia from oxygen poisoning.

Soybean roots contain (a) nitrogen-fixing nodules. Cells within the nodules are infected with Bradyrhyzobium japonicum, a rhizobia or “root-loving” bacterium. The bacteria are encased in (b) vesicles inside the cell, as can be seen in this transmission electron micrograph. (credit a: modification of work by USDA; credit b: modification of work by Louisa Howard, Dartmouth Electron Microscope Facility; scale-bar data from Matt Russell)

Mycorrhizae:  mutualistic relationship between fungi and roots

A nutrient depletion zone can develop when there is rapid soil solution uptake, low nutrient concentration, low diffusion rate, or low soil moisture. These conditions are very common; therefore, most plants rely on fungi to facilitate the uptake of minerals from the soil. Fungi form symbiotic and mutualistic associations called mycorrhizae with plant roots, in which the fungi actually are integrated into the physical structure of the root. The fungi colonize the living root tissue during active plant growth.

  • Ectomycorrhizal fungi have hyphae that wrap around the epidermal cells of the root.
  • Endomycorrhizal fungi (also called arbuscular fungi) have hyphae that can penetrate the cell walls (though not the cell membranes) of the plant root cells. Endomycorrhizae are found in the roots of more than 80 percent of terrestrial plants.

Through mycorrhization, the plant obtains nitrogen, phosphate, and other minerals, such as zinc and copper, from the soil. The fungus accesses these nutrients from decomposition of dead organic mater in the soil, making these nutrients biologically available to itself and to the plant. The fungus obtains nutrients, such as sugars, from the plant root. Mycorrhizae also help increase the surface area of the plant root system because hyphae, which are narrow, can spread beyond the nutrient depletion zone. Hyphae can grow into small soil pores that allow access to phosphorus that would otherwise be unavailable to the plant. The benefit to fungi is that they can obtain up to 20 percent of the total carbon accessed by plants, and the benefit to the plant is increased absorption of minerals. Mycorrhizae also function as a physical barrier to pathogens, and in some cases produce antibiotics which are secreted into the soil.

Root tips proliferate in the presence of mycorrhizal infection, which appears as off-white fuzz in this image. (credit: modification of work by Nilsson et al., BMC Bioinformatics 2005)