How Plants Use Nitrogen

Learn how complex nitrogen molecules are transformed into a substance that plants’ roots can access and use.

Red clover

Red clover provides a nitrogen-rich cover crop.

Photo by iStock/tamer

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Farmers, gardeners, and students of science all know that plants need an environmental supply of nitrogen to survive, much less thrive. Unlike carbon dioxide, which green plants can harvest from the gaseous atmosphere through photosynthesis, nitrogen gas (N2) isn’t available for plants’ aboveground parts to use. Instead, we growers apply nitrogen fertilizers to garden beds or manage soils with cover crops, green manures, and even animal manures to supply nitrogen in a form that plant roots can readily take up. To understand how nitrogen from the atmosphere can actually be used by plants, it’s helpful to expand our knowledge of nitrogen chemistry.

Nitrogen’s Properties

Symbol: N
Atomic number: 7
Atomic mass: 14.0067 u ± 0.0001 u
Electron configuration: 1s22s22p3
Electrons per shell: 2,5
Melting point: -346 degrees Fahrenheit
Boiling point: -320.4 degrees Fahrenheit

How Nitrogen Works in the Soil

Nitrogen atoms are energetically predisposed to exist as pairs of individual nitrogen atoms bonded tightly to one another. This is why we use the symbol N2 to represent the relatively nonreactive nitrogen gas (see infographic, below). It takes a lot of energy to split the nitrogen atoms apart. This is problematic for plant roots, which prefer to take up nitrogen in the form of the soluble nitrate ion (NO3¯), which is a negatively charged molecule consisting of a single nitrogen atom bonded to a trio of oxygen atoms (O). Other forms of nitrogen that you might find in your garden’s soil include the soluble, negatively charged nitrite ion (NO2¯) and the soluble, positively charged ammonium ion, which consists of a nitrogen atom bonded with four hydrogen atoms (NH4).

In simplified terms, the principal forms of nitrogen that plant roots can utilize are nitrates and ammonium. A group of fungi and bacteria called decomposers convert animal and plant waste in the soil into ammonium, and in exchange they extract energy to support their metabolism. Nitrogen-fixing soil bacteria — such as those found in the root nodules of legumes — also help create ammonium, and nitrifying bacteria convert ammonium ions into nitrite ions, which they in turn transform into nitrate ions that are finally available for uptake by plant roots. Denitrifying bacteria can convert nitrates to N2, which is then released into the atmosphere and is no longer available for plant root uptake (unless it re-enters the soil and begins the whole cycle over again).

In this simplistic version of the nitrogen cycle as it relates specifically to photosynthetic plants, you can see that it takes a while to pull nitrogen from complex forms, like proteins and nucleic acids, and that the process relies on different groups of soil organisms to make it happen. As you may imagine, the processes are not perfectly efficient and, therefore, some ammonium will be lost to the system.

At this point, it’s clear how important it is to compost organic matter in or on the soil to keep as much nitrogen in a place — and in a form — that can become available to plants. Nitrogen-fixing soil bacteria, such as Azotobacter, Bacillus, Clostridium, and Klebsiella certainly play an important role in getting atmospheric nitrogen back into the system, but in some plants there’s an even better way.

Fixing Nitrogen with Legumes

Farmers and gardeners generally know that plants in the bean family (legumes) are able to supply most, if not all, of their nitrogen needs. Legumes work in concert with a special class of nitrogen-fixing bacteria that pull nitrogen out of the atmosphere and supply it to the plant in a usable form after the bacteria have been enclosed in a special root structure called a “nodule” (see photo, above right). If this situation looks like a bacterial infection of the plant, at least on the surface, that's because it truly is. However, because the bacteria involved receive something back from the plant, the relationship is known as a mutualistic one, in which both organisms benefit. This mutualistic relationship is nearly as important in bringing atmospheric nitrogen into legumes as it is in supplying soil ecosystems with some of the nitrogen needed to thrive.

Here’s how this mutual relationship works: The legume seed germinates, and the root begins to grow. The root releases molecules that encourage specific species of the Rhizobium genus to colonize the root. The Rhizobium bacterial cells often attach to the fine cell hairs of the root’s outer layer. This causes the tiny hairs to deform, which facilitates penetration by a drinking-straw-like growth formed by the bacteria. When this so-called “infection-thread” reaches the root’s main structure, the plant is stimulated to grow a nodule through cell division that eventually encases the bacteria within a housing unit created from oxygen-tight root tissue. At this point, the Rhizobium no longer needs its protective cell walls and it becomes solely dependent on the plant to supply its energy and oxygen needs. In return, the bacteria provide the plant with much-needed nitrogen.

The fixing of atmospheric nitrogen, therefore, requires plenty of energy and tight control of the oxygen levels in the nodule. If there’s too much oxygen, then the fixation reactions can’t take place. If there’s too little oxygen then the bacteria won’t be able to metabolize. Also, contrary to popular belief, not all nodulated legumes can meet all of their own nitrogen needs. While some produce more nitrogen than others, the process is ultimately dependent on the plant species and on the relative success of root nodulation.

Very rarely does fixed nitrogen leak from nodulated legume roots into the surrounding soil. Rather, the nitrogen is used in the plant to build leaves and seeds that are high in protein. The benefit to the soil comes from the complex nitrogen compounds that are deposited in the soil when the plant dies and decomposes.

Because different legumes have different nitrogen-fixing bacterial species associated with them, it’s critical to know that your soil has the right type. The best way to ensure this is to plant inoculated seeds at least every few years to keep a population of the correct bacteria thriving in the soil. For small areas, it might also be possible to inoculate the soil directly in your garden.

There are other nitrogen-beneficial relationships between plants and soil bacteria, but none quite so profoundly intricate as the one found in legumes. Next time you wonder why it’s useful (even important) to inoculate your legume seeds or dig in a legume-rich cover crop, you’ll understand exactly how to build nitrogen levels in soil without adding any expensive amendments.


Oscar H. Will III (Hank) depends on a host of decomposers and nitrifying bacteria to keep his heirloom corn plots in tip-top shape. Between tons of sheep manure, hay compost, and leguminous cover crops, he hasn’t purchased nitrogen fertilizers for decades — and has built hundreds of tons of topsoil in the process.