Plants that fix nitrogen


Nitrogen in the Environment: Nitrogen Cycle

Scott C. Killpack and Daryl Buchholz
Department of Agronomy
Your browser does not support the video tag.

Nitrogen is important to all life. Nitrogen in the atmosphere or in the soil can go through many complex chemical and biological changes, be combined into living and non-living material, and return back to the soil or air in a continuing cycle. This is called the nitrogen cycle.

Figure 1
Oversimplifying, the nitrogen cycle works this way.

A basic look at the nitrogen cycle

Plants need nitrogen to grow, develop and produce seed. The main source of nitrogen in soils is from organic matter. Soils in Missouri commonly contain one to four percent organic matter. Organic matter largely arises from plant and animal residues. The nitrogen in organic matter is largely in organic forms that plants cannot use. Bacteria found in soils convert organic forms of nitrogen to inorganic forms that the plant can use. Nitrogen is taken up by plant roots and combined into organic substances in the plant, such as enzymes, proteins and chlorophyll. Chlorophyll gives the plant its green color. When the plant dies, it decays and becomes part of the organic matter pool in the soil. The basic nitrogen cycle is illustrated in Figure 1. It shows nitrogen changing from organic matter in the soil, to bacteria, to plants and back to organic matter.

  • Plant and animal wastes decompose, adding nitrogen to the soil.
  • Bacteria in the soil convert those forms of nitrogen into forms plants can use.
  • Plants use the nitrogen in the soil to grow.
  • People and animals eat the plants; then animal and plant residues return nitrogen to the soil again, completing the cycle.

Another way nitrogen enters the cycle is as inorganic nitrogen from the atmosphere and factories. The concern with these forms is that the incremental amount of nitrates they add to the nitrogen cycle may threaten groundwater.

  • Rain storms contribute atmospheric nitrogen through rain drops that reach the soil.
  • Legumes, such as soybeans, alfalfa and clovers, are plants that can convert atmospheric nitrogen into plant-usable nitrogen.
  • Factories that produce nitrogen fertilizers add nitrogen to the soil when farmers and gardeners “feed” their crops.
  • Nitrogen in sewage sludge from municipal waste plants can be used to fertilize farm fields.

Ways nitrogen is lost to the cycle

For the most part, the nitrogen cycle is soil based. Nitrogen is lost from the cycle in four ways:

  • Denitrification
    Bacteria change nitrate in the soil to atmospheric nitrogen, which joins the atmosphere.
  • Volatilization
    Turns urea fertilizers and manures on the soil surface into gases that also join the atmosphere.

Together, these first two processes account for most of the nitrogen lost to the cycle — a concern for soil fertility.

  • Runoff
    Carries the nitrogen in fertilizers and manure and the nitrogen in the soil into our rivers and streams — a concern for water quality.
  • Leaching
    Carries nitrates soo deep into the soil that plants can no longer use them, producing a dual concern — for lost fertility and for water quality, as nitrates enter the groundwater and the wells that provide our drinking water.

More about the nitrogen cycle

The largest single source of nitrogen is the atmosphere. It is made up of 78 percent of this colorless, odorless, nontoxic gas. However, plants are unable to use nitrogen as it exists in the atmosphere. Nitrogen from the air (N2) enters the nitrogen cycle through several unique types of microorganisms that can convert N2 gas to inorganic forms usable by plants. Some of these microorganisms live in the soil, while others live in nodules of roots of certain plants.

Nitrogen also can enter the cycle from other sources besides the air, manure and decaying plant materials. Nitrogen also can enter the cycle from the application of commercial nitrogen fertilizers.

Nitrogen can be lost from the cycle. It can be lost to the atmosphere, removed by harvesting crops or lost to surface water or groundwater. However it is lost, nitrogen can enter the cycle again through one of the processes discussed above or through other processes. These additional pathways of gains and losses to the nitrogen cycle are illustrated in Figure 2.

Figure 2
A more comprehensive look at the nitrogen cycle.

Impact on water quality

Nitrogen becomes a concern to water quality when nitrogen in the soil is converted to the nitrate (NO3-) form. It is a concern because nitrate is very mobile and easily moves with water in the soil. The concern of nitrates and water quality is generally directed at groundwater. However, nitrates can also enter surface waters such as ponds, streams and rivers. The presence of nitrates in the soil are largely the result of natural biological processes associated with the decomposition of plant residues and organic matter. Nitrates can also come from rainfall, animal manure and nitrogen fertilizers.

Whether or not nitrates actually enter groundwater depends on underlying soil and/or bedrock conditions, as well as the depth to groundwater. If depth to groundwater is shallow and the underlying soil is sandy, the potential for nitrates to enter groundwater is relatively high. However, if depth to groundwater is deep and the underlying soil is heavy clay, groundwater contamination from nitrates is not likely.

Once nitrates get into the groundwater, the greatest concerns are for infants less than one year old and for young or pregnant animals. High levels of nitrates can be toxic to newborns, causing anoxia, or internal suffocation. Seek alternative water sources if nitrate levels exceed the health standard of 10 ppm nitrate-N. Do not boil water to eliminate nitrates. It increases nitrate levels rather than decreasing them. The most common symptom of nitrate poisoning in babies is a bluish color to the skin, particularly around the baby’s eyes and mouth. These symptoms of nitrate toxicity are commonly referred to as the “blue-baby” syndrome.

The initial draft of this publication was written by Karen DeFelice, former associate extension agronomist; Nyle Wollenhaupt, former state extension agronomist; and Daryl Buchholz, state extension agronomist. This material is based upon work supported by the United States Department of Agriculture, Extension Service, under special project number 89-EWQI-1-9203.

How Much Nitrogen

Plants use nitrogen for many different functions. Without N, plants could not manufacture peptides, amino acids, proteins, enzymes, chlorophyll, or nucleic acids (the building blocks of DNA and RNA). These components are essential for plants to grow and function properly. The reactions that occur during photosynthesis require a lot of nitrogen. If N is deficient during photosynthesis, less chlorophyll is produced and plants begin to lose their green color (chlorosis). Turf responds to many stress conditions by producing special proteins and other metabolites that are rich in nitrogen. Inadequate access to N renders plants more susceptible to stress-related problems. On the other hand, excessive applications of nitrogen will also contribute to problems. Plants respond to abundant N by increasing top growth and arresting root growth. Free amino acids can linger in the leaves that can invite both foraging insects and disease pathogens. In addition, a guttation fluid that is rich in nitrogen and other nutrients can exude from the leaf tips-a phenomenon that is analogous to raising a banner that reads, “EAT AT JOE’S.” When the guttation fluid dries, the leftover salts can burn the leaf tips. Another potential for problems is that when plant growth is pushed by excess nitrogen, the production of their defense compounds is often suppressed.

Applying just the right amount of nitrogen is not only extremely important but it is almost impossible because conditions that determine the amount of N a plant needs at a given time are constantly varying. Air and soil temperature, moisture, HOC, the angle and intensity of the sun, and the variety of grass all affect the rate at which the turf plant will use nitrogen. The optimal amount of N today could be excessive or inadequate tomorrow. Plants have the ability to respond to both deficient and excess nitrogen but it is not always enough. When nitrogen is inadequate, plants produce sugars in the leaves that are quickly transported into the roots. These sugars feed roots and enable them to grow farther into the soil in search of more nitrogen. If too much N is available, the leaves produce amino acids which increases shoot growth. Sugar production is all but arrested and root growth is suppressed. This slows down the absorption of N through the roots.

Plants don’t understand the difference between nitrogen that is biologically released from organic sources and the soluble kind that is applied by modern superintendents. Nitrate is nitrate to the plant. But they also have a hard time understanding and adapting to the rags-to-riches scenario associated with many chemical-feeding programs. During periods when N is inadequate the plant responds by elongating roots. When, all of a sudden, a tidal wave of nitrogen is available from an application of soluble N and an abundance of roots absorbs more than the plant needs, some serious side-effects that include disease susceptibility, insect attraction, burning, and other problems can occur. In a healthy soil ecosystem, however, there are mechanisms that buffer and regulate the amount of N available to plants.

Many soil organisms need nitrogen more than plants but they need it balanced with a certain amount of carbon. This balance occurs in proteins that reside in organic residues and friable humus, and in the prey upon which many soil organisms feed. In fact, one of the main ways in which organisms make N available to plants is through predation of other organisms. Predators such as bacteria-feeding nematodes, for example, don’t need or want the amount of nitrogen inherent in their prey and release the excess as ammonium, which is biologically converted into nitrate that turf roots can absorb. Applications of compost or natural organic fertilizers compliment the functions of soil organisms and they, in turn, regulate the amount of N available to plants. This is not to say that soluble N should never be used but if it is the only source of nitrogen applied, biological activity will likely be suppressed to a point where nutrient regulation will be inadequate. There has to be available digestible carbon if soil organisms are going to regulate applied nitrogen. If the turf ecosystem is healthy and functioning properly, judicious applications of soluble N can be regulated by soil organisms. Many soil organisms can use soluble nitrogen, which, in turn, moderates the amount available to plants. As predation and other biological activities occur, more nitrogen is released for turf roots to absorb. Coincidentally, the activity level of the organisms that release N and other available nutrients respond to many of the same conditions that stimulate plant activity so the availability of nutrients is synchronized with need. Spoon-feeding soluble N is rarely as ideal.

If large doses of soluble N are applied, both plants and organisms can be overwhelmed. High salt fertilizers act like a sponge and draw moisture away from the surrounding area. This can cause osmotic shock, killing organisms in close proximity. Eventually, as the salt is dissipated within a greater solution, the dissolved nutrients change from harmful to helpful and can be absorbed by some soil organisms. Once assimilated into a living organism, the nutrient is somewhat stable until the organism dies or is preyed upon. If it dies, nitrogen may or may not be released depending on the saprophyte that consumes the remains. If the saprophyte requires less N than what is available from its food source, then some will be released; however, if it requires more, then nitrogen may be immobilized from other sources. In a turf soil, the former scenario is more likely than the latter. If a predator eats the organism, there is almost always a release of N in a form available to plants. Not only can this system increase nitrogen efficiency but it can also sustain the release of it for a longer period of time. Unfortunately, very little of this biological regulation will occur on a green constructed of sand, topdressed with sand, and fertilized purely with soluble salts. There needs to be healthy, active, well-fed and diverse population of soil organisms and this is next to impossible to maintain in an environment without adequate levels of organic matter. The sand based environment on most greens serves as an almost inert medium that provides mechanical support for the turf plants. It is rarely cultivated as a habitat for soil life. Old greens, however, may have accumulated enough organic matter over the years to provide adequate habitat for soil biology.

Developing a program that addresses the biological needs of the soil is a logical step toward improving fertility. The use of well-made, well-aged compost in the topdress mixture, compost tea in the irrigation system, and natural organic fertilizers in the spreader can not only reduce the need for soluble N but increase its efficiency as well. In other words, less soluble nitrogen can accomplish more. Applications of compost during spring and fall core cultivation incorporates valuable resources for a diversity of soil organisms. The addition of compost tea and natural organic fertilizers provide more nutrients and even some inoculation. If soluble N is still needed, small doses can react synergistically with biological functions that increase overall nitrogen efficiency. It may not be needed, however. Well-made, mature compost can contain anywhere from 1/2 to 3 percent nitrogen depending on the feedstock from which it was made. Don’t expect a great flush of growth, however. The release of N from compost is slow and sustained and depends on factors such as temperature and moisture. If turf is growing in a very cold soil, some soluble N may be necessary to fulfil the plants’ needs until the soil warms up.

Natural organic nitrogen is synonymous with protein. One of the reasons that it is more expensive than its chemical cousin is that it has a greater value in the animal feed and pet food markets than it does as fertilizer. Protein is not an available nutrient for plants. The chemical structure of protein is too large and complex to be assimilated through plant roots. Protein can, however, be assimilated by soil organisms. When proteinaceous materials come in contact with the soil, organisms begin dismantling it into amino acids and peptides. Most of the nitrogen and carbon is consumed and temporarily immobilized but some is released and mineralized by other organisms into simple nitrogen ions that plant roots can absorb. The population of saprophytes that consumed the protein grows exponentially which results in a relative increase in the number of predator organisms that feed on them. The result of this increased predation is an increase in available nitrogen for plant roots but the release is steady and sustained unlike the tsunami of pabulum that is typical of soluble fertilizers. An additional advantage to using proteinaceous nitrogen is that it is extremely efficient. Very little if any is ever lost to leaching, volatilization, or denitrification and the corresponding increase in biological activity can often reduce plant susceptibility to disease infection and attractiveness to some foraging insects. Taking into consideration its efficiency and its ability to nurture an active soil food web (which can lead to significant savings elsewhere), the value of natural organic nitrogen can be considered more relative to its price.

Even though golf course conditions aren’t found anywhere in nature, contemporary fertilization practices do not in any way resemble natural feeding phenomena. The use of soluble, available nutrients bypasses the digestive system of plants, i.e., the living biomass in the soil. A fertility program that ignores the needs of these organisms is, in a sense, repudiating their value and importance. The assumption that these soil organisms have little to no worth may be the main reason why managers in both agriculture and horticulture are so dependent on chemicals.

The preceding text was excerpted from Ecological Golf Course Management, published by John Wiley & Son, 2002

Problems With Over-Mulching Trees and Shrubs

Mulching trees and shrubs is a recommended cultural maintenance method with many benefits, yet it can literally kill plants if mulch is applied improperly. A mountain of mulch, piled high against the tree trunk, does not kill a tree immediately—it results in a slow death. Over-mulching is a waste of mulch (and money!). It is a leading cause of death of azalea, rhododendron, dogwood, boxwood, mountain laurel, hollies, cherry trees, ash, birch, linden, spruce, and many other landscape plants.

Over-Mulching Can Kill

How does over-mulching kill trees and shrubs? The most common causes are:

Oxygen Starvation

Suffocation of the tree roots is the most common cause of tree and shrub death from overmulching. Repeated applications can contribute to waterlogged soil/root zone by slowing soil water loss via evaporation. With water occupying most soil porespace, air content is mimimal and diffusion of oxygen is essentially blocked. Roots need oxygen for respiration. When soil oxygen levels drop below 10%, root growth declines. Once too many roots decline and die, the plant dies.

When shallow rooted plants are planted in mounds of mulch, oxygen levels can begin to decline below plant needs. This is especially common in the spring and the fall, which are critical periods for root growth, and during other wet periods. Oxygen deprivation is also prevalent in soils that do not have good drainage.

Symptoms may take several years to appear, depending on the plant and the soil type. Symptoms include offcolor, yellowing foliage (chlorosis), abnormally small leaves, poor twig growth, and dieback of older branches. Unfortunately, by the time the symptoms are noticed, it is generally too late to correct the problem. At this point, the plant is usually in a state of irreversible decline, and will most likely die.

Inner Bark Death of Aboveground Root Flares

Inner bark (phloem) death comes from the piles of mulch placed directly against the stems/trunks of trees and shrubs. The root flare stem and trunk tissue is quite different from root tissue—it cannot survive a continually moist environment, and must be able to breathe through lenticels. When mulch is piled near trunks, gas exchange decreases, stressing and ultimately killing the inner bark (phloem) tissue. This also occurs when trees are planted too deep (the root flare is buried). Phloem death may also occur when pop-up sprinkler heads continually saturate the mulch placed against the plant’s trunk.

Once the inner bark dies, roots become malnourished and weakened, with a subsequent reduction in water and nutrient uptake. The entire health of the plant is thus affected. If such wet conditions continue long enough, the phloem tissue may die, starving the roots since they then receive none of the essential photosynthates produced by the leaves.


Most fungal and bacterial diseases require moisture to spread and reproduce. Trunk diseases gain a foothold into the moist, decaying bark tissue under the mulch. Once established, the disease organisms ultimately invade the inner bark, starving the plant, and finally kill the plant. Often this scenerio is accompanied by bark beetles and borers, that are also attracted to stressed plants, expedite the decline, and also allow entrance of other fungal pathogens into the plant.

Excess Heat

The wet mulch layers piled up next to the trunk may begin to heat up when the bark begins to decompose. This scenerio is similiar to composting, where temperatures within inner mulch layers may reach 120° to 140° F. This high heat may directly kill the inner bark/phloem of young plants, or may prevent the natural hardening off period that plants must go through in the fall in preparation for the winter. If the trunk flare tissue is not sufficientlly hardened off before freezing weather arrives, the tissue may die, the roots may starve, and the plant will decline.

Other Drawbacks of Over-Mulching

The soil pH, or acidity level, may also be changed by the continuous use of the same type of mulch. In particular, pine bark mulch is quite acidic (pH of 3.5 to 4.5), and can cause the soil to become acid with constant use year after year. After the soil becomes acidified, some nutrients are not available to the plant, and others, such as iron, manganese, and zinc, become readily available at high, toxic levels. Symptoms of micronutrient toxicity mimic those of Phythopthora wilt. Sometimes, plants cannot tolerate micronutrient toxicity, becoming stressed and killed by secondary disease organisms and insects.

On the other hand, hardwood bark is initially acidic, but ultimately may cause the soil to become too alkaline (basic), causing acid loving plants (such as azaleas and rhododendron) to decline because of micronutrient deficiencies of iron, manganese and zinc. Symptoms appear as yellowing of foliage, often with prominent green veins. To avoid the above mentioned problems, regularly check the soil pH and rotate the type of mulch used.

Piles of mulch next to the trunk may also provide cover for chewing rodents such as mice and meadow voles. These rodents live under the warm mulch in the winter and chew on the nutritious inner bark. This often goes unnoticed until the following spring when the “tree doesn’t look good.” If the trunk is girdled (>50% chewed around the trunk), there is little that can be done to save the plant outside of bridge grafting.

“Fresh,” or non-aged (uncomposted) mulches may cause nitrogen deficiencies in many young plants. Decomposing bacteria need an amble supply of nitrogen to break down the mulch. Since bark mulches have little nitrogen available, the bacteria utilize the soil nitrogen. This process may cause nutrient deficiencies, especially if the mulch is mixed down into the soil and is of a fine texture. Look for symptoms of leaf yellowing on new growth. This is considered a temporary condition.

Standard Mulch Recommendations

Mulch may thus be one of the best or one of the worst things you can do for your plants. Mulch depth should standardly not exceed 3 inches. However, on poorly drained soils, mulch depths should not exceed 2 inches, especially for shallow rooted plants. Wet soils may not need any mulch. Coarser textured mulches can be placed a bit deeper due to better oxygen diffusion into the soil. Finer textured mulch, such as double shredded mulch, may need only a 1- or 2-inch layer.

If you have a problem with excess mulch, dig through the landscape to see how deep the mulch really is. A light raking of existing mulch may be all that is needed to break through the crusted or compacted layers that can repel water. Pull mulch back from plant stems and trunks—a rule of thumb is 3 to 5 inches away from young plants, and 8 to 12 inches away from mature tree trunks. Visually look for the presence of a root flare; if not visible, at least some may be partially buried and must be exposed. Remove all soil or mulch up to the junction of the roots and trunk collar (taking care not to damage the tender bark) to expose the root collar. Leave the resulting well open and exposed to air. Research shows that an amazing number of plants have rapidly improved in color and vigor within months of root collar excavations.

In conculsion, mulch may be “worth its weight in gold,” but it must be applied properly for it to pay off (and not cause damage).


C. Carlson. 1998. Off the Leaf newsletter #303. (May/June).

April 2000

Copyright © 2020 Rutgers, The State University of New Jersey. All rights reserved.

For more information:

Cooperating Agencies: Rutgers, The State University of New Jersey, U.S. Department of Agriculture, and County Boards of Chosen Freeholders. Rutgers Cooperative Extension, a unit of the Rutgers New Jersey Agricultural Experiment Station, is an equal opportunity program provider and employer.

Nitrogen Fixing Bacteria with Peas, Beans and Family

Are Nature’s Nitrogen Factory

Nitrogen fixing bacteria are nature’s main method of changing nitrogen to plant available forms. It occurs underground in a very friendly symbiotic relationship of legume plant with Rhizobium types of bacteria. So Nature’s nitrogen factory could look something like this lupine field in Glacier National Park.

© Yasushi Tanikado |

It’s only been in the last century that man was even able to make synthetic nitrogen fertilizer using a process developed by Fritz Haber. To manage that we need to create super high temperatures and pressures in large fertilizer plants such as the one at Severnside in the UK shown here.

Recent research at the Center for Ecology and Evolutionary Biology at the University of Oregon by Dr. Jennifer Fox, found that agrichemicals such as synthetic nitrogen fertilzers and pesticides, interfere with the communication between plants and nitrogen fixing bacteria. The result is less nitrogen is fixed by the bacteria and of course more synthetic nitrogen is needed to maintain yields. YIKES! another vicious cycle.

Farmers and Gardeners Harness Nature’s Nitrogen Production

Ancient farmers wouldn’t have known about nitrogen fixing bacteria, but they did know that growing legumes yielded good food and helped other crops grow. In fact, of the eight Neolithic founder crops – the first plants domesticated by man – four were legumes and included lentils, peas, chickpeas, and bitter vetch.

Like our ancient ancestors, modern farmers plant legumes to in effect grow a type of nitrogen rich fertilizer for their other crops. It isn’t the peas and beans that are making the fertilizer though, it’s the nitrogen fixing bacteria, various Rhizobium, that actually do the nitrogen fixing.

These bacteria colonize the roots of their preferred plant partner. From their homes in the plant roots they take nitrogen from the air and convert it into ammonia, a form of nitrogen that plants can use. For this valuable service the legumes feed the bacteria a steady diet of plant sugars.

Your soil may already have several varieties of rhizobia present that live on from year to year. Pull up a bean plant and check it for white or pinkish white nodules on the roots.

I just did this myself in the community garden plot where I grow vegetables. The whole garden here is regularly rototilled at both the beginning and end of the season. Unfortunately, while this looks neat, tidy and ready to plant, it really does a number on the soil life. The bean plant roots didn’t have a single nodule.

While you will still get a crop from the seed you sow both soil and crop are improved if the right nitrogen fixing bacteria are present in the soil.

It’s worth using a legume inoculant in the following cases:

  • Where the topsoil has been removed. The rhizobium bacteria are certain to be completely nonexistent or very reduced in this case.
  • Where the soil has not had any legume ground cover for a long time. Rhizobium can lie dormant for a few years, however, they will eventually die off unless they are united with their appropriate legume host.
  • In soils where synthetic fertilizers and pesticides have been heavily used. These agrichemicals are toxic or caustic to rhizobium bacteria.
  • When planting a variety of legume that hasn’t been grown in your garden before.
  • As insurance. Inoculants aren’t expensive and it never hurts to supply your seed with a fresh batch of the right bacteria. Share the cost with your neighbor if cash is really tight.

How to Use Legume Inoculants

The Right Stuff

– Make sure you have the right type of nitrogen fixing bacteria inoculant for the crop you are growing. Many seeds used for cover crops are “rhizocoated” meaning it is already coated with the right nitrogen fixing bacteria. If the seed is raw – meaning not coated – buy the appropriate inoculant when you buy your seeds.

Often garden stores stock an inexpensive inoculant containing several types of nitrogen fixing bacteria. This mix most often contains the bacterium strains for peas and beans and will work well for them. However, if you are planting peanuts for example it won’t work for them.

It’s Alive – But Not Forever

– The powder containing the nitrogen fixing bacteria is a live product. It has an expiry date and needs to be stored properly to ensure it is viable. If in doubt get a fresh batch.

Moisten Seed to Apply

– Moisten the seed with either a little water or milk. Add the powder to the seed and mix thoroughly so that the seed is completely covered.

Use Lots

– You can’t use too much of the rhizobacteria, but you can use too little, so pile it on.

Maybe You’ve Got ’em, Maybe Not

– Once you have a specific nitrogen fixing bacteria in the soil it may be present for future crops. But you must plant its host regularly so the bacterium have a place to live. Otherwise they will eventually die out. It’s probably worth inoculating every year to be sure.

List of Common Legumes and Their Rhizobium Bacteria

  • Peanut – Bradyrhizobium sp.
  • Milkvetch – Rhizobium sp. (Astragalus)
  • Chickpeas – Mesorhizobium sp.
  • Lassen crownvetch – Rhizobium sp.
  • Soybeans – Bradyrhizobium japonicum
  • Chickling vetch, grass pea – R. leguminosarum bv. viciae
  • Lentils – R. leguminosarum bv. viciae
  • Bird’s foot trefoil – Mesorhizobium loti
  • Lupines – Bradyrhizobium sp. (Lupinus)
  • Alfalfa – Sinorhizobium meliloti
  • Sweet Clover – S. meliloti
  • Common Beans – R. leguminosarum bv. phaseoli
  • Field or Garden Peas – R. leguminosarum bv. viciae
  • Crimson, Red, White and Alsike Clover – R. leguminosarum bv. trifolii
  • Hairy Vetch, Fava Beans, Broad Beans – R. leguminosarum bv. viciae

Won’t My Compost Supply the Nitrogen Fixing Bacteria I Need?

In a word No. This is one of the rare situations where compost isn’t going to help.

Your compost pile is a home for decomposer bacteria and fungi. The decomposers can circulate and help maintain plant available nitrogen in your garden. But they can not take nitrogen from the air and turn it into fertilizer.

Rhizobium, the nitrogen fixing bacteria equipped to do that, need live hosts. If the legume along with its bacteria partner have not grown in the soil before it doesn’t matter how much compost you add it’s not going to put that microbe in your garden.

Other Nitrogen Fixers

If you have green plants you likely have some sort of nitrogen fixing bacteria at work. We think it’s all about legumes but it turns out that it’s just that those Rhizobium bacteria are some of the few types of bacteria kind enough to survive lab conditions.

Now that we have relatively cheap gene sequencing available researchers are finding that many types of bacteria living in the soil have the gene for fixing nitrogen.

Other Pages You Might Enjoy

Actinomycetes are another group of bacteria. These ones are more famous for giving us many of our antibiotics, but one group of them is an important nitrogen fixing bacteria.
Soil Crusts are very young soils found in deserts, alpine areas and other extreme climates. Here cyanobacteria or blue-green algae are the nitrogen fixing bacteria.
The Haber Process brings us synthetic nitrogen fertilizer. It’s said to feed a third of the world but it has some big downsides.

  1. Compost Home
  2. Soil Bacteria
  3. Nitrogen Fixing Bacteria

  1. Compost Home
  2. Nitrogen Cycle
  3. Nitrogen Fixing Bacteria


Let’s face it; green beans are taken for granted. Vegetable gardening articles typically feature the queen of the garden, the tomato, or some exotic greens, or a new technique, or trendy tools. Yet year after year the dependable green bean appears in most every supporting cast, faithfully producing crops and feeding the gardening world. Green beans are the blue collar vegetable of our Texas Gardens.
Beans are perhaps the easiest veggie of all to grow. If you want to get kids hooked on gardening, let them help plant and harvest a crop of green beans. They are among the fastest of veggies from seed to table. Their large seed size makes planting with fumbly little fingers fool proof. And the hide-and-seek task of harvesting beans holds kids attention quite well.
Perhaps it is just this dependable, easy character that causes them to be taken for granted. Well, whatever the cause, they deserve an award for their integral role in any great vegetable garden. While other veggies may fly or flop in a given year, you can pretty much count on green beans to provide a dependable harvest.
First A Little “Beanology”
Before we get into the specifics of bean culture, let’s take a brief look at some “beanology.” Basically the term bean is pretty generic and refers to the seed pods of many different plants in the legume family, including many ornamentals. In the vegetable garden, beans may be grouped into three basic categories, based on the maturity of the pod at harvest and the part eaten.
Green beans, also called snap beans and string beans, are grown to harvest the fleshy pods before the seeds inside develop. Shell beans are grown for the fresh seeds. They are allowed to grow a bit longer, usually until the pods start to turn yellow and soften, when they are harvested for their immature but plump, fresh seeds. Dry beans are also grown for the seeds but are usually allowed to mature further, sometimes to the point of drying on the bush. They are then harvested, shelled (and fully dried if necessary) and then stored for later use.
Green beans originated in Central America. By the time Columbus arrived they had spread through Mexico and into North America. From here they were taken back to the Old World where they joined other types of beans in vegetable gardens.
In this article we will focus on green, those harvested for their fleshy pods. I grew up referring to them as “string beans,” a throwback to the early varieties that had tough strings running down the pod sutures that had to be removed before the pods were cooked.
I recall years past as a child spending an evening stringing and snapping the day’s harvest in a bowl on my lap while watching TV. Those were often pinto beans, a dried bean that can also be harvested when young as green beans. But the green bean quality of pintos is pretty low compared to our modern varieties, and most new varieties are stringless. A great development, especially considering the fact that there’s not much worth watching on TV these days anyway.
Preparing A Garden Spot
Beans like sunlight. While they will tolerate a little shade, like most fruiting vegetables they need at least six hours of sunlight to do their best. They also like good drainage. Sandy loam soils are best, but if you have a heavy clay all is not lost. Simply mix in lots of compost and build raised beds to facilitate drainage. These veggies do not like wet feet, and will flounder and rot in a soggy clay during extended rainy spells.
Green beans are tolerant of moderately fertile soil. They prefer a pH range of about 6.0 to 7.5. If your soil is more acidic, a little lime can easily fix the problem. In high pH soils, beans may exhibit a little iron chlorosis, which shows up as yellowing of the new growth.
To remedy iron chlorosis, add some iron sulfate or chelated iron to the soil according to label directions. Iron sulfate tends to tie up in the soil fairly quickly and becomes unavailable to growing plants. Chelated iron is more resistant to tie up, but is more expensive. For an even better long-term solution, add some compost whenever you work the soil prior to planting. Compost helps balance your soil nutrient content and stimulates microbes that cycle nutrients in the soil.
The most significant nutrient problem for beans is excessive nitrogen in the soil. High nitrogen levels stimulate top growth and will delay and reduce production. Beans are legumes and therefore are able to produce their own nitrogen through a symbiotic relationship with certain bacteria on their roots. These bacteria form nodules that are attached to the sides of their roots. They can extract nitrogen from the air in the soil and fix it into a form that the bean plants can use.
If your soil is really poor, mix in a cup of complete fertilizer before planting. Otherwise such additions are probably not necessary. Once the soil has been built up with compost for a couple of seasons, such supplements are usually not needed.
Beans love warm temperatures and will not perform well at all if planted too early in the spring. For you scientific gardeners, they need the soil temperature to be at least 65 degrees to sprout quickly and grow vigorously. In cold soil they will just sit there and never amount to much of anything. Wait until at least about a week after your last average frost date before planting.
You can get in a second planting or two about 10 to 14 days apart. This will extend the harvest season. However, when temperatures heat up, beans will fail to set very well and those that do will form smaller pods and be of poorer quality.
In late summer there is another planting window for the fall crop. This is truly the prime bean season. Pods that ripen in the cooler days of fall are at their peak of quality!
If you are growing beans in a new garden spot, it may be worthwhile to purchase a seed inoculant to make sure the symbiotic bacteria are present. Wet the seeds and then place them in a small paper sack. Then pour the black, dusty inoculant powder into the sack and shake it around a bit. This will get some of the powder on the seeds. Plant the inoculated seeds immediately.
Once you have grown beans in a garden spot, these inoculants are not really needed as the soil contains plenty of the symbiotic bacteria. I have planted and grown beans quite successfully in a new garden area without inoculants. The nitrogen-fixing bacteria are often present from other legumes which grew in the area.
To plant the seeds, open a trench about an inch or so deep with the corner of a hoe. Drop the bean seeds in the trench about 2 inches apart. No thinning will be necessary at that spacing. Cover the trench with about an inch of soil and tamp it down gently to firm the soil around the seeds. Then water the planting row well to moisten the soil deeply. I usually plant beans in two rows spaced about a foot apart down the length of the bed.
Keep the soil moist while waiting for the seedlings to emerge. This will reduce crusting and help get the seeds off to a fast start. Wait to mulch until the seedlings are about 6 inches tall. Unmulched soil warms up faster and mulch may attract certain pests that will feed on the emerging seedlings.
Once the new plants are about 6 inches tall, it is time to add mulch. If they lack vigor and green color, a light fertilization may be helpful. Apply 1/2 cup of balanced fertilizer per 25 feet of row in a 3 inch deep trench about 6 inches away from each row of plants. Then cover the fertilizer with soil and water it in well. After watering, apply a couple of inches of mulch to protect the soil and prevent it from splashing onto the plants.
After that, simply keep the plants moderately moist to prevent drought stress. They really do not need a lot of supplemental water, especially if well mulched; soggy conditions are very detrimental.
I have grown many different varieties of beans over the years. Most have done quite well. There are some proven choices, but I encourage gardeners to experiment and include a new variety or two with an old reliable variety each year. You will find many great new varieties are waiting for you to discover them.
I group green beans into four basic types: standard round-podded beans, flat-podded “Italian” beans, French filet beans (haricot verts) and pole beans.
The most common type in our Texas gardens is the standard round-podded types. One that is an old standard with Texas gardeners is ‘Contender.’ This bean consistently produces nice crops of good quality pods and does well in many different soils and climates. I have conducted trials for a number of years and although ‘Contender’ has never been the winner in productivity, it was always in the top group. I think if you are going to plant just one variety it is a good choice, and is widely available.
Other great bush beans include ‘Jade’ (my personal favorite), ‘Derby’ (1990 All-America Selections), ‘Florence,’ ‘Topcrop’ (1950 All-America Selections), ‘Provider,’ ‘Espada,’ and ‘Dorabell’ (yellow wax type).
Flat-podded Italian or Roma type beans produce large crops of large, flat, full-flavored green beans. Great varieties include ‘Roma II,’ ‘Romano,’ and ‘Romanette.’
French filet beans are thin, tender beans considered as gourmet fare by bean connoisseurs. I find them very tasty but a bit tedious to pick since it takes more to make a meal. Some choice varieties are ‘Maxibell,’ ‘Normandie,’ and ‘Nickle.’
Pole beans are a great way to take advantage of tight garden space and to spread the harvest season out a bit. My favorite pole bean is ‘Kwintus’ (formerly called ‘Early Riser’), a very early bean with flattened pods that speed from seed to harvest in just 45 days. Three other proven pole varieties in my gardens are ‘Northeaster’ (another favorite with large, flat pods), ‘McCaslan’ (slightly flattened pods) and ‘Rattlesnake’ (round pods). I have grown all four and found them to be outstanding yielders of quality beans and much superior to the pole types ‘Kentucky Wonder’ and ‘Blue Lake.’
Pole beans climb by twining around a support. Bamboo poles, wire mesh fencing, livestock panels, lattice work and even twine dropped from the eaves of your home to the soil line will make a great support for pole beans. Just make sure that they, like bush types, are in an area that receives plenty of sunlight.
Pests and Diseases
Beans have their enemies in the garden. Perhaps the most troublesome are spider mites. These pests love a dry, hot, dusty environment and tend to gather on the lower surface of leaves where their feeding causes discoloration and, in serious cases, drying and death of the leaves. They can be identified by placing a white piece of paper beneath leaves showing the light colored mottling that is characteristics of mite infestations. Then thump the leaves. Watch the paper for mites, which appear as tiny specks moving about.
When mites start to become a problem direct a spray of insecticidal soap upward from beneath the plants. Make this application early in the morning when temperatures are still moderate and the sun is not baking down on the plants. A repeat application five to seven days later may be needed for better control.
Aphids can also gather and feed on bean plants. While I have yet to experience a significant aphid problem on my bean crops, if they do become troublesome they can be controlled with insecticidal soap or pyrethrum sprays.
Stink bugs can deform pods. They are more difficult to control but insecticide products are available that will control them. I prefer to simply break off any damaged pod sections and have not found them to be serious enough in most seasons to warrant spraying.
The most common bean diseases are damping off, rust and powdery mildew. Damping off refers to the decay and destruction of young seedlings by fungal diseases. It is best managed by keeping the seed bed well drained and not too soggy wet. Avoid turning under fresh green matter just prior to planting beans. Also allow the soil to warm in the spring before planting the seeds.
Rust is a fungal disease that causes reddish powdery spores to appear on the lower leaf surface as well as on the pods. It is made worse by frequent wetting of the foliage and harvesting the plants when the foliage is wet. Powdery mildew causes a white, powdery dusting on the leaves and will result in drying and loss of foliage. It is not a common problem on beans but can occasionally do significant damage. Both rust and powdery mildew may be controlled by minimizing wetting of the foliage and by sprays of wettable sulfur.
Beans may be harvested at any time from when the pods are very small to when they reach their full length. Quality is less if you allow green beans to stay on the plant too long, so it is best to not allow the beans inside to develop past about a third of their full size.
You can get a feel for this as you look at the outside of the pods. Although varieties differ significantly in shape and form, when the beans in the round-podded types are bulging visibly in the pods, those pods are probably getting too mature. Fresh pods are very tender and snap in two readily when bent. You will need to harvest almost three times a week to prevent some pods from over maturing. They really move fast, come harvest time!
When harvesting, use two hands, one to hold the plant where the bean attaches and the other to pull on the pod. Bean plants are very brittle and can easily be broken or uprooted during harvest. Finally, allow the morning dew or irrigation to dry off the foliage before harvesting to avoid spreading foliage disease.
Each planting of beans should yield pods for a couple of weeks. After harvest is over, you can pull up the plants and compost them. I prefer to cut them off at ground level and leave the roots (with their nitrogen fixing nodules) in the soil to release nutrients back into the soil.
Green beans are a moderate source of protein, fiber, vitamin C and beta carotene (a precursor to vitamin A). They are low in calories and contain a modest supply of calcium and folic acid.
Fresh green beans are flavorful and add color to our mealtime. Purple-podded varieties turn dark green with cooking and yellow-podded types fade a bit. The key to tasty green beans is to not overcook them or they will become mushy and lose their bright color.
Simply steam or boil them in a little water for a short amount of time. It only takes about 5 minutes for them to become tender and ready to eat. Cook them just long enough for them to be barely cooked through but yet still retain the slightest crunch.
Oh yeah, this is Texas, so feel free to add onions and bacon to taste!

“It doesn’t take much to see that the problems of three little people doesn’t add up to a hill of beans in this crazy world,” Humphrey Bogart famously said in the movie Casablanca. For the farmers and breeders around the world growing the common bean, however, ensuring that there is an abundant supply of this legume is crucial, both for its importance in cropping systems to ensure plant vitality and for food security. Moreover, the U.S. Department of Energy Office of Science has targeted research into the common bean because of its importance in enhancing nitrogen use efficiency for sustainability of bioenergy crops, and for increasing plant resilience and productivity with fewer inputs, on marginal lands, and in the face of the changing climate and environment.

Thought to have originated in Mexico, the common bean was domesticated separately at two different geographic locations in Mesoamerica and the Andes. (Roy Kaltschmidt, LBNL)

All plants require nitrogen to thrive, and nitrogen fixation is the process by which atmospheric nitrogen is converted into ammonia. However, many agricultural lands are deficient in nitrogen, leading farmers to rely on fertilizers to supply the needed nutrient for their crops. According to the U.S. Department of Agriculture, the United States imports more than half of the nitrogen used as fertilizer, a total of nearly 11 million tons in 2012. Kidney beans, navy beans, string beans and pinto beans are all varieties of the common bean, which ranks as the 10th most cultivated food crop worldwide. Legumes such as the common bean and soybean, however, can form symbiotic relationships with nitrogen-fixing bacteria. Understanding how such symbiotic relationships are formed and sustained is a crucial to improving agricultural practices as increasing crop yields are desired both for fuel and food production.

To this end, a team of researchers led by Scott Jackson of the University of Georgia, Dan Rokhsar of the U.S. Department of Energy Joint Genome Institute, Jeremy Schmutz of the DOE JGI and the HudsonAlpha Institute for Biotechnology and Phil McClean of North Dakota State University sequenced and analyzed the genome of the common bean, Phaseolus vulgaris. The project was supported by the U.S. Department of Energy and the National Institute of Food and Agriculture, U.S. Department of Agriculture, and the work was published online June 8, 2014 in the journal Nature Genetics.

“Unlocking the genetic make-up of the common bean is a tremendous achievement that will lead to future advances in feeding the world’s growing population through improved crop production,” said Sonny Ramaswamy, director of USDA’s National Institute of Food and Agriculture. “While we have much to learn about the application of genomics in agriculture, this study is groundbreaking. I applaud the work of this team of scientists and look forward to their continued work in this important area.”

For the study, the team sequenced and assembled a 473-million basepair genome of the common bean. Though it is thought to have originated in Mexico, the common bean was domesticated separately at two different geographic locations in Mesoamerica and the Andes, diverging from a common ancestral wild population more than 100,000 years ago. The team then compared sequences from pooled populations representing these regions, finding only a small fraction of shared genes. This indicated that different events had been involved in the domestication process at each location.

Legumes such as the common bean and soybean can form symbiotic relationships with nitrogen-fixing bacteria. Understanding how such symbiotic relationships are formed and sustained is a crucial to improving agricultural practices as increasing crop yields are desired both for fuel and food production. (Roy Kaltschmidt, LBNL)

The team looked for regions associated with traits such as low diversity, flowering time, and nitrogen metabolism. They found dense clusters of genes related to disease resistance within the chromosomes. They also identified a handful of genes involved in moving nitrogen around. This information could be beneficial for farmers practicing the intercropping system known as milpa, wherein beans and maize or, occasionally, squash, are planted either simultaneously or else in a relay system where the beans follow maize. The practice ensures that the land can continue to produce high-yield crops without resorting to adding fertilizers or other artificial methods of providing nutrients to the soil.

The team then compared the high quality common bean genome against the sequence of its most economically important relative, soybean. They found evidence of synteny, in which a gene in one species is present in another. They also noted that the common bean’s genome had evolved more rapidly than soybean’s since they diverged from the last common ancestor nearly 20 million years ago.

“Improvement of common bean will require a more fundamental understanding of the genetic basis of how it responds to biotic and abiotic stresses,” the team concluded. “These findings provide information on regions of the genome that have been intensely selected either during domestication or early improvement and thus provide targets for future crop improvement efforts.”

Phil McClean presented on the common bean genome project at the recent 9th Annual DOE JGI Genomics of Energy & Environment Meeting. Watch the video at

The Phaseolus vulgaris genome data are available publicly through the DOE JGI’s comparative plant genomics portal known as Phytozome, now in its 10th revision (

This short article is a chapter from my book “Fertilizer for Free: How to make the most from Biological Nitrogen Fixation”.

One important question permaculture designers should ask themselves:

Is there anything you can do to increase the rate of biological nitrogen fixation?

The benefits of having more nitrogen rich organic matter in the soil are myriad. Starting with:

  • higher general productivity
  • richer and more diverse soil life
  • more available phosphorus
  • higher availability of various other nutrients
  • higher capacity to hold nutrients

Fortunately there’s actually quite a lot you can do to make sure your plants are growing the fastest and they fix the most nitrogen! Here are nine methods you can use in your permaculture design to make sure your nitrogen-fixing plants are giving you and the whole ecosystem more benefits.

Method 1 — choose the right species

The first method you should use if you want to increase biological nitrogen fixation is choosing the right species of nitrogen-fixing plant for your climate. This step is very important, as some species fix nitrogen more efficiently than others. Good candidates for efficient nitrogen-fixing plants in a temperate climate are:

  • ground cover: lupines, cowpea, fava bean, vetch, clover, alfalfa (on good soil)
  • tall trees: black alder, black locust, empress tree
  • shrubs and short trees: Autumn olive, gumi, Siberian pea shrub, Russian olive, sea berry

Method 2 — right amount of plants

Usually the amounts of nitrogen fixed per hectare (or acre) are expressed by how much nitrogen certain plants fix if they grow in monoculture. That means that the whole area is covered in certain types of nitrogen-fixing plants.

Young trees and shrubs take up much less space than mature trees and shrubs. So if you want your soil to get a lot of nitrogen you should have the entire area or almost the whole area covered in nitrogen-fixing plants.

Planting a few hundred little trees per acre or per hectare will not give you a lot of nitrogen for a few years, until the canopy covers more area.

One way to ensure you are going to fix a lot of nitrogen from year one in agroforestry or forest gardening settings is to plant nitrogen-fixing trees or shrubs and also plant nitrogen-fixing cover crops.

Method 3 — inoculate your plants with the right nitrogen fixing bacteria

If the field in which you want to plant your forest garden or establish a perennial pasture has not grown any legumes in the last three years, you should inoculate your seeds or seedlings. Some nitrogen-fixing plants require different species of bacteria than the other, so you need to get an inoculant specific to the species you are going to plant. If you can’t find the right legume inoculant you might use some soil from the ground around a healthy nitrogenous plant of the particular species.

To check if a certain plant is inoculated you need to dig out the plant’s root and check for bacteria nodules. If it has nodules it means there are at least some nitrogen-fixing bacteria. That’s good enough, so you can take a few shovels of that soil to add to the “nitrogen fixation enhancing compost” you will be using later. If you plant bare root seedlings you will see if there any nitrogen-fixing nodules or not on the seedlings you are planting, so you can evaluate whether or not you need legume inoculant.

Sea-berry — nitrogen fixing plant proven to fix up to 180kg of nitrogen in poor, sandy soil

Method 4 — right pH and calcium level

Nitrogen-fixing bacteria need a high calcium level to work efficiently. Nitrogen-fixing plants for temperate climates grow the best in soil with a pH of 6.4 with adequate level of calcium. Your soil should have minimum of 1500 lbs. of calcium per acre in the top 7″ of your soil (1500 kg per hectare in the top 18 cm).

Just because your nitrogen-fixing plants are growing doesn’t necessarily mean they are fixing nitrogen for themselves, or even creating a surplus for other parts of the ecosystem! If you want optimum nitrogen fixation rates you need to have sufficient calcium in the soil.

If the soil pH is low, consider adding some lime. If liming your soil is not possible add finely ground limestone to the planting holes (if you are planting trees or shrubs).

If your pH is high, but the calcium level is low (for example because your soil has a lot of magnesium or sodium) consider adding calcium sulfate dihydrate (CaSO4•2H2O). Don’t worry, it is just gypsum! It will provide your soil with calcium without raising pH.

Method 5 — adequate phosphorus level

I highly recommend checking the phosphorus level of the soil. If the available phosphorus is low, consider adding some source of phosphorus to the soil. If you are planning to add soft rock phosphate or any other (natural) source of phosphorus, add it to the compost or manure and incorporate it into the field. If you are planting shrubs or trees you might want to add some compost or manure to the planting hole. In the future, higher nitrogen levels will help to make more phosphorus (and other minerals) available for the plants, but by making sure there is available phosphorus at the beginning it will speed up the whole process. I recommend making sure you have at least 200lbs/acre or 200kg/ha of phosphorus in the top 7″ of your soil (top 18cm). If rock phosphate is not available and your soil needs it, add some diammonium phosphate (DAP). If financial constraints do not allow you to add the full amount of soft rock phosphate or DAP, apply as much as you can afford. Even a dose of just 20 kg DAP per hectare (20 lbs. per acre) can make a difference to your young nitrogen fixing plants. With time and larger sized plants, and with mycorrihiza fungi inoculation and efficient nitrogen fixation, they will be able to make phosphorus that’s already in the soil available. But that’s in the future; your plants need phosphorus now to make the process efficient. So think about it as an investment.

Method 6 — proper soil molybdenum level

Molybdenum is one of the essential nutrients plants require for growth. It is critical for nitrogen fixation. A low soil molybdenum level means low nitrogen fixation level….

Molybdenum is easily available for plants around a pH of 6.4. It’s more difficult for plants to get molybdenum in low pH soils (below pH 5.5). Quite often sandy, acidic soils are deficient in molybdenum. Make sure you have at least 1ppm (2kg per hectare or 2 lbs per acre) of molybdenum in your soil for optimum biological nitrogen fixation. If your soil levels are lower you can use the following methods to make sure your pioneer plants have enough molybdenum for optimum nitrogen fixation:

  • add 3 oz. per acre (90 grams per acre or 180 grams per hectare) of sodium molybdate as foliar spray
  • use 1 oz. for 1 acre (60 g for 1 hectare). Use either molybdenum trioxide or ammonium molybdate as a seed treatment. You can mix your seed treatment with the legume inoculant, but do it just before you are going to sow your seeds.

Bill Mollison recommended using molybdenum as fertilizer (if necessary) in Permaculture – A Designers’ Manual (page: 194, 197).

If you don’t want to test your soil for molybdenum, you can plant nitrogen-fixing plants anyway. If you recently added lime, or if you have pH around 6.4, chances are you will not need to add this essential micronutrient.

Method 7 — add some rock dust

Add some rock dust to the soil. It contains micronutrients and trace minerals. They are proven to enhance the growth of trees and shrubs, including the nitrogen fixing ones. You can use basalt rock dust, granite rock dust, azomite, or simply rock dust from a local quarry. If you are planting trees, add a handful of rock dust to the pit you are planting your nitrogen fixing trees or shrubs in, to make sure your plants are going to have a healthy start. You can also add some rock dust to the “nitrogen fixation enhancing compost”.

Method 8 — add some beneficial microbes to your soil

This method of increasing biological nitrogen fixation is based on making sure you add a broad range of beneficial microbes and fungi. They are important especially for the long term success of a sustainable ecosystem, as they make nutrients more available to the plants, especially phosphorus.

This will increase both the speed and growth of nitrogen-fixing shrubs, trees and herbaceous plants.

You need them especially if your are planting your nitrogen-fixing trees on land that was used for conventional agriculture. There are many commercial products on the market that contain beneficial organisms. You can also make some actively aerated compost tea yourself.

Method 9 — don’t use pesticides and help your soil to get rid of pesticides residues

A lot of pesticides have a bad influence on soil biology, including nitrogen-fixing bacteria. For example glyphosate (the active ingredient in Monsanto’s Roundup herbicide) is very detrimental to nitrogen-fixing bacteria. On top of that glyphosate ties up many trace elements in the soil — mainly: manganese, iron and zinc — that might slow down the growth of your plants if the level of those elements is low. This effect is especially predominant on sandy soils. The solution is simply to not use pesticides, especially not the conventional ones. If necessary (as indicated by your soil test) add required amounts of manganese, iron and zinc. It is especially useful on sandy, acidic or very acidic soils. To some degree it will help to overcome limitations of your current soil conditions.

On the other hand a clay soil might contain more residues of pesticides that were used up to a few decades ago, some of which were already banned 30 years ago! To combat this, increase organic matter and soil activity and hope that some microbes and fungi will eventually decompose those harmful ingredients. All previous methods will also expedite this process.

How do you make nitrogen fixation enhancing compost?

Get a or create a pile of rich and mature compost. Add required amount of rock phosphate and rock dust. For every 10 parts of compost you can add:

  • 1 part of rock phosphate
  • 1 part of rock dust
  • required amount of beneficial microbes (mycorrihiza fungi, actively aerated compost tea, etc.)
  • 1 part of topsoil from a place where nitrogen fixing plants of the species you want to grow are already growing (and fixing nitrogen).

Mix it all together and spread it on top of your soil. Recommended rate: minimum 1 ton per acre (2 tons per hectare). If you are planting trees or shrubs you might want to put one shovelful of this compost in the soil pit where you will be planting your trees.

Do you have any other tips about helping nitrogen fixing plants to thrive and provide you with more biologically fixed nitrogen for free?


If you like this article, please consider buying my ebook: Fertilizer for Free: How to make the most from Biological Nitrogen Fixation.

Nitrogen is one of the most important elements in growing a productive, successful garden. Without enough nitrogen, plant will struggle and die.

Below I have compiled the best nitrogen fixing plants list just for you! These are the best nitrogen fixing plants for you to grow in your vegetable garden rotations, permaculture garden or food forest settings.

Please read: This information is provided for educational purposes only and is not intended to treat, diagnose or prevent any disease. We encourage you to make your own health care decisions in partnership with a qualified health care professional.

This post contains affiliate links, this means at no extra cost to you, we make a commission from sales. Please read our Disclosure Statement

What are Nitrogen Fixing Plants?

Nitrogen fixing plants are plants that work with bacteria in the soil to capture the atmospheric nitrogen and convert it to bioavailable nitrates that the plants can use to grow.

Nitrogen fixing plants are great to use as a cover crop or green manure in the vegetable garden, or as a chop-and-drop addition to food forest areas.

Benefits of increasing nitrogen in the soil

The benefits of having more nitrogen rich organic matter in the soil include:

  • higher general productivity
  • richer and more diverse soil life
  • more available phosphorus
  • higher availability of various other nutrients
  • higher capacity to hold nutrients

How can I add nitrogen to my soil naturally?

Some organic methods of adding nitrogen to the soil include:

  1. Adding composted manure to the soil.
  2. Planting a green manure crop, such as borage.
  3. Planting nitrogen fixing plants
  4. Adding coffee grounds to the soil.

What type of plants fix nitrogen?

Generally speaking, legumes are what you are after if you want to fix nitrogen in to the soil. There are other nitrogen fixing plants, but not all of other families of other plants are nitrogen fixers. So if in doubt, plant a legume! Otherwise there is quite a substantial list of nitrogen fixing plants below.

How do plants fix nitrogen?

Nitrogen fixing plants don’t actually pull nitrogen from the air on their own. They need help from a common bacteria called Rhizobium. The bacteria infects legume plants such as peas and beans and uses the plant to help it draw nitrogen from the air. You can see the little rhizomes on the plants roots, they look like little nodules.

There are two other bacteria that work with non-legume plants to help fix bacteria as well, these are the Frankia (works with the Actinorhizal plants) and the cyanobacteria.

What are the best nitrogen fixing plants?

The most commonly used nitrogen fixers are clover, beans, peas and lupins. This is because they are easy to obtain, the grow fast and tolerate most climates.

There are however, many many other plants that fix nitrogen in the soil. These range from cover crops, to herbs, to flowers to whole trees!

The best Nitrogen Fixing Plants to grow in your Permaculture Garden or Food Forest

Here are the best nitrogen fixing plants for your garden or food forest, they are split in to plant types, then listed alphabetically. Click here for a downloadable PDF version.

Nitrogen fixing trees

Autumn olive
Black Locust
California mountain mahogany
Cape Broom
Cherry silverberry
Chinese Yellow Wood
Chinese licorice
Evergreen laburnum
Golden chain tree
Inga tree (tropical)
Japanese Pagoda
Kentucky Coffee Bean
Laburnum trees
Locust tree
Mesquite trees
New Jersey Tea
Persian silk tree
Purple Coral Pea Shrub
Redbud/judas tree
Russian Olive
Siberian Pea Shrub
Silverberry (Elaeagnus x ebbingei)
Silverthorn/thorny olive
Silver wattle
Tamarind (tropical)

Nitrogen fixing cover crops / green manures

Alfalfa (perennial)
Asparagus pea
Bean, Fava/Bell
Bean, Hyacinth
Bean, Jack
Bean, Velvet
Birds Trefoil (perennial)
Clover, Arrowleaf
Clover, Balansa
Clover, Berseem
Clover, Crimson
Clover, Mammoth Red (perennial)
Clover, New Zealand White (perennial)
Clover, Red (perennial)
Clover, Subterranean
Clover, Sweet (perennial)
Clover, White (perennial)
Lespedeza, Annual
Lespedeza, Serciea (perennial)
Pea, Field
Pea, Winter
Peanut, Perennial (perennial)
Sun Hemp
Velvet Bean
Vetch, Bigflower
Vetch, Chickling
Vetch, Common
Vetch, Hairy

Nitrogen fixing flowers

Bladder Senna
Californian lilac
Chinese wisteria
Dyers greenweed
Earthnut pea
Glandular senna
Indigo (all Indigofera genus)
Purple Coral Pea Shrub
Spring pea
Tree lupin
Wisteria, American
Wisteria, Japanese
Wisteria, Kentucky

Nitrogen fixing edible food plants / vegetables

Nitrogen fixing herbs

Licorice, American
Licorice, European

Nitrogen fixing vines

Bean, Scarlet Runner
Bean, Wild Groundnut
Groundnut, Fortune’s
Groundnut, Price’s
Hog Peanut
Kudzu (Japanese arrowroot)
Pea, Beach
Pea, Butterfly
Pea, Earth-Nut
Peas, Vining Garden Peas
Vetch, American
Vetch, Bitter
Vetch, Tufted
Vetch, Wood
Wisteria, American
Wisteria, Japanese
Wisteria, Kentucky

Don’t forget to grab your pdf list of nitrogen fixing plants here.

Please pin and share with your friends!

Do you need more delicious goodness fresh from the farm?

Sign up for our weekly Fresh From the Farm Newsletter

All goodness, no spam.

Get exclusive content, discounts and updates.

You have Successfully Subscribed!

And don’t worry, we hate spam too! You can unsubscribe at anytime.

Is Nitrogen Fixation Oversold with Legume Cover Crops?

One expected benefit of using legumes as a cover crop is to provide a source of nitrogen (N) to the cropping system. However, when legumes are included in mixtures with grasses and broadleaves for a relatively short growing period, the amount of actual fixed N may be relatively low. Even when planted as a monoculture or legume-only mixture, the amount of fixed N may be lower than anticipated.

Figure 1. Legumes vary in the amount of biomass and nitrogen they provide. Shown above are two legume-based cover crops: Cowpea (left) and a grass mix (right) with cowpea as one of its components.

The N fixation process is a chemical reaction facilitated by Rhizobia bacteria in root nodules that convert atmospheric N (N2) to ammonia (NH3). This process uses energy produced by the legume plant during photosynthesis. The ammonia is almost immediately converted to ammonium (NH4). Using the N in ammonium and the carbohydrates from photosynthesis as energy, plant proteins are formed and become part of legume plants. It is important to note it can take up to six weeks after planting before N fixation begins.

Many factors determine the amount of nitrogen (N) that can be fixed by different legumes used as cover crops or forage cover crops:

  • Different legumes fix different amounts of N.
  • Legumes must form effective root nodules to fix N.
  • Legumes often use available soil N for growth before beginning to fix N.
  • Well-established legumes fix more N than do seedling legumes.
  • Legumes do not have equal biomass yield potential.

Together, this means that different legumes and different legume growth environments provide greatly different amounts of fixed N.

Little information is available on the amount of N that is fixed when legumes are grown as cover crops. Much information has been generalized from forage and pasture studies of mixed stands of grasses and legumes. In mixed perennial grass-legume pastures, reported values for suitable legume stands of clovers and vetches often range from 50 to 100 pounds fixed N per acre for annual N fixation of legumes in mixed pastures.

Most reported fixed N rates are for a full year of growth from full stands of monoculture legumes. Well-established perennial legumes, including red and white clover, have been reported to provide 75 to 200 pounds fixed N per acre. This compares with alfalfa, which provides 150 to 200 pounds fixed N per acre.

Legumes behave much like grasses when soil N is available and will use that before fixing additional N. This means that legumes can scavenge N from the soil just as grasses do. That N can be released back to the soil later for use by succeeding crops as the legume biomass decomposes. The amount released will depend primarily on the concentration of N in the legume biomass and the amount of biomass produced.

On average, summer annual legumes, including cowpea, mungbean, soybean, and sunn hemp, typically have the lowest N concentrations of the legumes. When mature, these are often around 2% N (12% to 14% crude protein). Winter annual legumes, such as crimson clover and the vetches are often around 3% N (18% to 20% crude protein). Some perennial pasture legumes such as red clover, white clover, and alfalfa can have up to 4% N (25% crude protein).

Other factors can further reduce the amount of N provided by legumes:

  • Poor growing conditions can reduce legume biomass yield and fixed N contribution.
  • In some cover crop mixtures, legumes are not major contributors to overall biomass production.

For example, Austrian winter pea and cowpea are two legumes commonly used as cover crops or included in cover crop mixtures. In pure stands with poor growing conditions, biomass yields are often less than 1500 pounds per acre. With a concentration of 2% N, less than 30 pounds N per acre would be fixed. Typically, biomass yields from legumes in excess of 1500 pounds per acre are required to provide appreciable amounts of fixed or scavenged N.

As long as legume cover crops are not harvested, nearly all the fixed and scavenged N eventually becomes available to subsequent crops. Very little N remains in the soil while plants are actively growing. This N is available for uptake by both legumes and other non-legume species.

Snow: Poor Man’s Fertilizer

  • This year’s first snowdrops were recently covered with yesterday’s snow. Click on other pix to enlarge and read the captions.Photo/Illustration: susan belsinger
  • The vegetable garden under a blanket of snow; life is burgeoning below the surface.Photo/Illustration: susan belsinger
  • Garlic has sprouted below this protective layer of wheatstraw and cover of snow.Photo/Illustration: susan belsinger
  • Narcissus, daffodils and Virginia bluebells are patiently waiting for spring temps.Photo/Illustration: susan belsinger
  • This Hellebore, also known as the Lentan Rose, has opened up in its timely manner, as it does each year. It is amazing how this plant can freeze and thaw and still keeps blooming.Photo/Illustration: susan belsinger

Is this familiar adage an old wive’s tale?

In fact, snow does contain nitrogen and other particulates like sulfur, which it collects as it falls through the atmosphere, however so do rain, sleet and hail, and believe it or not, lightning. Rain and lightning contain more nitrogen than snow. Statistics from agricultural studies estimate that as a result of snow and rainfall averages, between 2 to 12 pounds of nitrogen are deposited per acre in the U.S. per year.

A blanket of snow, when the ground is frozen, is like a layer of protective mulch. Its insulative properties protect both the soil and the plants from desiccating winds and freezing temperatures. It also helps to insulate the plants as they “heave” which can expose their roots to air, as the soil freezes and thaws throughout the winter.

According to Jeff Lowenfels: “There is something else that happens when it snows: nitrogen is deposited by the snow and absorbed either into the soil food web residing and active at low temperatures or by plants as a result of nitrogen fixation, a microbial activity which, astonishingly enough, can take place even at low temperatures.”

If the earth is saturated, the rain runs off; if the ground is frozen, the snowmelt will also run off and most of the nutrients will not be absorbed. In the spring when the earth has thawed and we have a snow, this blanket of snow protects newly emerging plants and leaches nutrients like nitrogen slowly, as it melts into the earth.

Fall-planted bulbs, and bulbs like tulips and garlic that need cold temperatures to grow can benefit from a cover of snow which provides moisture and fertilization and prevents frost heave. Some folks actually heap snow on garden beds with bulbs or around newly planted trees for extra protection and insulation.

Tim Travers further explains nitrogen in his article “Though we live in a sea of it – nitrogen gas makes up 78 percent of our atmosphere – plants and animals can only use nitrogen when nitrogen gas becomes “fixed” into the usable form of nitrate (when oxygen is bonded with the nitrogen) or ammonium (when hydrogen is bonded with the nitrogen.) Most of this nitrogen fixing is carried out by specialized anaerobic bacteria living cooperatively inside the root nodules of legume plants – peas, beans, and locust trees – and other pioneer species like the speckled alder. Once it’s fixed, nitrogen is taken up quickly by plants and cycled through the biosphere from air to soil to living organisms and back. As a result, there isn’t much available nitrogen left in soil – it’s too valuable.”

Although, we gardeners are antsy for warm weather and our hands in the soil, let us welcome these last snows and rainfall; the precipitation will nourish our gardens in the coming spring.

When it snowed in Brooking, SD in the early spring of 2013 they received 9 inches of snow . This contained the equivalent of about 2 inches of water. The nitrate-N content of the snow was 0.4 ppm while the ammonium-N content was 0.3 ppm. This was equivalent to only 0.3 pounds-per-acre of available nitrogen. Not exactly a windfall of nitrogen, but also very typical nitrogen precipitation concentrations for this area.
The National Atmospheric Deposition Program (NADP) has measured nitrogen and other nutrients in precipitation for a number of stations around the country for over 30 years. The annual level of nitrogen deposits from precipitation will range from about 5 pounds-per-acre on the Western edge of the Corn Belt to 12 pounds-per-acre in the Eastern Corn Belt.
Why the difference? Contrary to common perceptions, most of the nitrogen in precipitation does not come from lightning. There are two main forms of N in precipitation – nitrous oxides (nitrate-N) and ammonium N. About 5-10% of the nitrous oxide forms originate naturally (i.e. lightning) and the remainder comes from human activity, such as emissions from motor vehicles, electric power plants, and industrial sources. Ammonium –N in precipitation can originate naturally from soil microbe activity (about 20%) while the remainder comes from manure or fertilizer (mostly urea forms) emissions of ammonia. The ammonium forms can make up from 25 to 75% of the total N in precipitation. Since most N in precipitation is from human activity, there tends to be higher levels occurring nearest large cities with industrial centers and near agricultural areas.
While the added N in precipitation is not a large contributor to the N needs of our major crops, it can cause large changes in some environments. Some plants can be favored over others by the larger N additions. Acid rain, which is a result of more N and S in rainfall, can cause changes in some freshwater ecosystems as well as harm some forest plant species. For more information on nitrogen deposition check out the National Atmospheric Deposition Program website.
The bottom line? Most snowfalls contribute little to our overall crop N needs, but can significantly influence some sensitive ecosystems.

Snow PROVIDES SOIL MOISTURE crops need to grow. Winter snowfall helps during the growing season because of the stored moisture that works its way down into the soil as the snow melts. No-till farming helps to trap snow and REDUCES DRIFTING. This allows for more even distribution of water into the soil as the snow melts. A layer of snow on winter wheat fields INSULATES THE DORMANT CROP. Wheat that is not protected by a blanket of snow can die—known as “winter kill”—in bitterly cold temperatures. An old saying about late spring snowfall is that it is “Poor man’s fertilizer.” Snow CONTAINS TRACE AMOUNTS OF NITROGEN from the atmosphere. The nitrogen will act as fertilizer for the next crop.

The amount of water in snow varies. A common rule of thumb is that ten inches of snow equates to 1 inch of water, or 10:1. This is true for snow that falls when the surface temperature is about 30ºF. If ground temperatures are between 33 and 36 ºF, the snow is “wetter.” In this case, about 8 inches of snow can contain 1 inch of water. Wet snow is often called “heart attack snow” because it is so heavy to shovel. If the entire atmosphere is 20ºF or colder the ratio may be closer to 30:1, or 30 inches of snow equaling 1 inch of water. This snow is lighter, and “drier.” The USDA Agricultural Research Service (ARS) studies snow using “low temperature scanning electron microscopy,” or incredibly powerful microscopes operated at freezing temperatures. This allows scientists to predict the amount of water that will be available to agriculture from snowpack.

From DeKalb County Farm Bureau’s Connections Publication

Nitrogen Nodules And Nitrogen Fixing Plants

Nitrogen for plants is vital to the success of a garden. Without sufficient nitrogen, plants will fail and will be unable to grow. Nitrogen is abundant in the world, but most of the nitrogen in the world is a gas and most plant cannot use nitrogen as a gas. Most plants must rely on the addition of nitrogen to the soil in order to be able to use it. There are a few plants that love nitrogen gas, though; they are able to draw the nitrogen gas from the air and store it in their roots. These are called nitrogen fixing plants.

How Do Plants Fix Nitrogen?

Nitrogen fixing plants don’t pull nitrogen from the air on their own. They actually need help from a common bacteria called Rhizobium. The bacteria infects legume plants such as peas and beans and uses the plant to help it draw nitrogen from the air. The bacteria converts this nitrogen gas and then stores it in the roots of the plant.

When the plant stores the nitrogen in the roots, it produces a lump on the root called a nitrogen nodule. This is harmless to the plant but very beneficial to your garden.

How Nitrogen Nodules Raise Nitrogen in Soil

When legumes and other nitrogen fixing plants and the bacteria work together to store the nitrogen, they are creating a green warehouse in your garden. While they are growing, they release very little nitrogen into the soil, but when they are done growing and they die, their decomposition release the stored nitrogen and increases the total nitrogen in soil. Their death makes nitrogen for plants available later on.

How to Use Nitrogen Fixing Plants in Your Garden

Nitrogen for plants is essential to your garden but can be difficult to add without chemical assistance, which is not desirable for some gardeners. This is when nitrogen fixing plants are useful. Try planting a winter cover crop of legumes, such as clover or winter peas. In the spring, you can simply till under the plants into your garden beds.

As these plants decompose, they will raise total nitrogen in soil and will make available the nitrogen for plants that are unable to get nitrogen from the air.

Your garden will grow greener and more lush thanks to plants that fix nitrogen and their beneficial symbiotic relationship with bacteria.

Globally, each year 120 million tonnes of nitrogen fertiliser is applied to crops worldwide to provide this nitrogen demand.

An incredible 48% of protein in the human diet comes from plants grown using artificial nitrogen fertiliser, but production and application of these fertilisers is unsustainable.

Some plants, such as the legumes, do not depend on these soil compounds or their chemical synthetics. Over thousands of years they have developed intimate symbiotic relationships with bacteria such as rhizobia. In exchange for sugars produced by the plant, these bacteria take nitrogen gas in the air and convert it into a form that the plant can use directly. This close entwinement of two biological organisms means that legumes get their nitrogen from the air rather than the soil.

Our scientists work on many aspects of understanding how this complex partnership occurs, with the aim of conferring the ability to fix nitrogen into crop species beyond legumes.

A step-by-step guide to nitrogen fixation

  1. Some bacteria that live in the soil fix nitrogen using the enzyme nitrogenase. Some are free-living. Others form symbioses with plants such as legumes, for instance the bacteria Rhizobia
  2. Rhizobia sense signalling compounds, such as flavonoids, that are released by the plant into the soil
  3. Rhizobia respond by activating Nod genes, which produce proteins involved in creating nodulating factor (nod)
  4. Nod factor is then perceived by the plant and causes root hairs to bend and trap the bacteria. It triggers internal oscillations and cell divisions within the plant
  5. Rhizobia grow inside the root hair and spread into other cells in the plant root forming what is known as an infection thread. The association between the bacteria and root forms the nodule

Nitrogen Fixation and the Nitrogen Cycle

In a symbiotic relationship with the soil bacteria known as ‘rhizobia’, legumes form nodules on their roots (or stems, see figure below) to ‘fix’ nitrogen into a form usable by plants (and animals). The process of biological nitrogen fixation was discovered by the Dutch microbiologist Martinus Beijerinck. Rhizobia (e.g., Rhizobium, Mesorhizobium, Sinorhizobium) fix atmospheric nitrogen or dinitrogen, N2, into inorganic nitrogen compounds, such as ammonium, NH4+, which is then incorporated into amino acids, which can be utilized by the plant. Plants cannot fix nitrogen on their own, but need it in one form or another to make amino acids and proteins. Because legumes form nodules with rhizobia, they have high levels of nitrogen available to them. Their abundance of nitrogen is beneficial not only to the legumes themselves, but also to the plants around them. There are other sources of nitrogen in the soil, but are not always provided at the levels required by plants, making the symbiotic relationship between legumes and rhizobia highly beneficial. In return for the fixed nitrogen that they provide, the rhizobia are provided shelter inside of the plant’s nodules and some of the carbon substrates and micronutrients that they need to generate energy and key metabolites for the cellular processes that sustain life (Sprent, 2001). Nodulation and nitrogen fixation by rhizobia is not exclusive to legumes; rhizobia form root nodules on Parasponis Miq., a genus of five species in the Ulmaceae (see ‘Rosales’).

Click on an image to view larger version & data in a new window

The picture on the left shows typical root nodules, these from bur clover (Medicago). The picture on the right shows “stem” nodules on Sesbania rostrata – stem nodules are produced from lateral or adventitious roots and are typically found in those few water-tolerant legume groups (Neptunia, Sesbania) that prefer wet or water-logged soils (Goormachtig et al., 2004).

The nitrogen cycle (shown below) describes the series of processes by which the element nitrogen, which makes up about 78% of the Earth’s atmosphere, cycles between the atmosphere and the biosphere. Plants, bacteria, animals, and manmade and natural phenomena all play a role in the nitrogen cycle. The fixation of nitrogen, in which the gaseous form dinitrogen, N2) is converted into forms usable by living organisms, occurs as a consequence of atmospheric processes such as lightning, but most fixation is carried out by free-living and symbiotic bacteria. Plants and bacteria participate in symbiosis such as the one between legumes and rhizobia or contribute through decomposition and other soil reactions. Bacteria like Rhizobium, or the actinomycete Frankia which nodulates members of the plant families Rosaceae and Betulaceae, utilize atmospheric nitrogen and convert it to an inorganic form (usually ammonium, NH4+) that plants can use. The plants then use the fixed nitrogen to produce vital cellular products such as proteins. The plants are then eaten by animals, which also need nitrogen to make amino acids and proteins. Decomposers acting on plant and animal materials and waste return nitrogen back to the soil. Human-produced fertilizers are another source of nitrogen in the soil along with pollution and volcanic emissions, which release nitrogen into the air in the form of ammonium and nitrate gases. The gases react with the water in the atmosphere and are absorbed by the soil with rain water. Other bacteria in the soil are key components in this cycle converting nitrogen containing compounds to ammonia, NH3, nitrates, NO3-, and nitrites, NO2-. Nitrogen is returned back to the atmosphere by denitrifying bacteria, which convert nitrates to dinitrogen gas.

Click on an image to view larger version & data in a new window

The Nitrogen Cycle. This image is a work of an Environmental Protection Agency employee, taken or made during the course of an employee’s official duties. As works of the U.S.federal government, all EPA images are in the public domain. The nitrogen cycle.

Leave a Reply

Your email address will not be published. Required fields are marked *