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A. 8. The Nitrogen Cycle and the Soil Food Web
A. 8. The Nitrogen Cycle and the Soil Food Web
A complete understanding of the nitrogen (N) cycle is necessary in order to comprehend why the soil foodweb is so important in being able to predict N cycling. Most people with little or no understanding of environmental microbiology do not do justice to the role of biology in N cycling. So, we need to go through this with most people.
Start with atmospheric N
The predominant form of N on this planet is nitrogen gas in the atmosphere. Seventy-five percent of the atmosphere is nitrogen gas, so the trick is getting that nitrogen into a form that plants can use.
N fixation
Back before life on Earth started, most of the N was fixed through the action of lightening, enough to get life started. After life started on earth, most of the nitrogen fixed is by microorganisms, and indeed, all N fixation requires the help of bacterial enzymes. Most people know about N-fixing bacterial genus, Rhizobium, on the roots of legumes. These bacteria make the plant form nodules to house them, allowing the bacteria to exclude oxygen, allowing the N-fixing enzymes to perform their function of converting N-gas into biomass.
But a number of other N-fixing bacteria abound in certain environments. Cyanobacteria form filaments, and are typically photosynthetic, so the bacteria fixing their own carbon from carbon dioxide also fix N inside those filaments, in many different extreme environments.
Free-living N-fixing bacteria, such as Azotobacter and Azospirillum, also fix N in the root systems of many different plants. The plant supplies the sugars that these bacteria need, in the amounts they need to perform N-fixation. So, while not truly symbionts, these bacteria usually are most active in the rhizosphere.
N is in bacterial biomass after N-fixation occurs
There is a mis-conception that Rhizobium, or the free-living N-fixing bacteria “dump” nitrate into the soil. They do no such thing. These bacteria require a great deal of energy to fix N. Fixed N does not get made into nitrate, or any other inorganic form of N. The bacteria fix N for themselves first, and is put into protein in the bacterium before anything else occurs. If the bacterial colony fixes enough N rapidly enough so the bacterial demand is met, then protein is provided to the plant, in the case of Rhizobium. The free-living bacteria are not in the plant, but in the rhizosphere, so all the fixed N remains tied up in bacterial biomass, in the form of protein mainly.
No inorganic N is dumped into the soil then, in this first step of fixing N. The plant may receive some N, but the plant isn’t going to give away N for no reason. Only when the plant dies will it lose N, and that N is in the dead plant litter, roots, seed, fruit, etc. This organic matter is elevated in protein N, but that form is not usable by other plants. It has to be decomposed by bacteria and fungi before anything else can happen.
No inorganic, plant-available N is released into soil through the process of N-fixation. The dominant form of fixed N is protein. How does that form of N get converted into ammonium, nitrite or nitrate?
Bacteria don’t die of old age in the soil. Neither do fungi. Empty hyphal strands may be left behind, but there is extremely little N in cellulose, or mannin, or chitin, or the other structural cell wall materials left behind as the empty tubes of fungal biomass. There is no evidence that in healthy soil any of these organisms die just because they get old. In lab cultures bacterial colonies will get old and the toxic metabolites that accumulate in the Petri dish will kill the bacteria in the colony. But that doesn’t happen in the real world. Water washes away the metabolites in the real world, or another kind of bacteria, or fungus, or other organisms eats that waste metabolite. So the colony doesn’t get stuck dying from it’s own excrement. The major reason bacteria or fungi die in soil is because someone eats them.
The Mineralization Step
Predator-prey interactions in soil are no different than in the aboveground world with cats and mice, hunting dogs and birds, tigers and water buffalo, lions and gazelle. Bacteria get eaten by protozoa, nematodes, earthworms, microarthropods, etc. When bacteria, with a C:N of 5 get eaten by a protozoan with a C:N of 30, possibly higher, then N, P, S, etc will be released in plant available forms.
If you are unfamiliar with these interactions, please read some of the reference materials in the reading list, or on Dr. Ingham’s list of publications, or attend some of her classes, or other soil ecologist classes.
When fungi are eaten by protozoa, nematodes, microarthropods and earthworms, N is released in a mineral form into the soil. The majority of this process of making plant-available N occurs in the rhizosphere of the plant. But mineralization occurs only because of biological processes.
Want to predict how much N will be mineralized? You have to understand how much N is being tied-up by the bacteria and fungi in non-leachable forms, how much will be leached and lost from the root system, and how much prey (bacteria and fungi) will be consumed by the predators (protozoa, nematodes, microarthropods, earthworms, etc). There are different flow rates for different organisms, so the relationship is not straightforward.
But if you do not understand biology, and do not know how much of whom is present, or how active they are, prediction of N-mineralization is impossible. It remains a black box, highly variable and head-scratching in its inability to be understood or predicted.
Initially N is in the form of ammonium
The predators of course release predominately ammonium, a nutrient that plants can take-up. But ammonium is not a good nutrient for ALL plant species. In general, ammonium is the right form of N for perennial plants, although all perennial plants that have been tested can take up nitrate and possibly a little nitrite as well.
But perennial plants growing with mostly nitrate in the root zone are HIGHLY prone to disease. Nitrate in high concentrations stresses these plants, and result in an never-ending battle with disease, requiring the use of high amounts of fungicide, nematode, antibiotic, and herbicide applications to combat the organisms being selected and enhanced by the high nitrate present.
Annual plants are best at using nitrate, although there is evidence that nitrate in high concentrations is harmful to continuing root function even with annuals. Annuals can take up ammonium, but generally help the equilibrium shift from ammonium to nitrate so the form of N they like is at least present, so they can preferentially take that form up.
How do you maintain ammonium as ammonium? Or convert it to nitrate?
Conversion to nitrite and then nitrate
In soil where the nitrifying bacteria are able to grow, these bacteria convert ammonium to nitrite and then nitrate. But nitrifying bacteria have some significant constraints on where they will grow. They need reduced oxygen conditions to do best. They typically reduce oxygen around their colony, so the bacterial individuals in the middle of the colony are in reduced oxygen conditions. Or they grow in the rhizosphere, where the rapid growth of all those other bacteria sets the stage for a small colony to be at the oxygen level they need. Nitrifiers take the hydrogen ions from ammonium and replace them with oxygen. Ammonium is first converted, by the action of bacterial enzymes, to nitrite (NO2) and then another set of bacteria converts nitrite to nitrate (NO3). It is an oxidation step of the nitrogen.
But this is not a mineralization step. Ammonium is already a mineral form of N, and so conversion to nitrite and then to nitrate is merely a shift in the form of inorganic N.
Nitrifying bacteria require particular habitats in order to grow and perform their nutrient cycling processes. These bacteria need the hydrogen ions in order to generate energy through their metabolic pathways. They remove H from the medium. What does that do to soil pH?
Nitrifying bacteria remove ammonium, and produce nitrate. They aren’t taking up the N, that are just using it to deal with the electrons they need to get rid of in respiration. In order to grow and perform their function, they will drive a soil more alkaline. As they utilize H ions during metabolic functions, the soil will become more alkaline.
Some scientists say that bacteria couldn’t possibly have that much effect on soil. Each individual bacterium is so small, how could bacteria have much effect on anything in soil? These people clearly don’t understand soil, or how many bacteria are in soil. In a healthy soil, there are 600,000,000 individual bacteria per TEASPOON, or gram, of soil. In conventional ag soil, there may be only 1,000,000 individual bacteria per gram of soil.
Consider that the only reason there is enough oxygen in the atmosphere of this planet for aerobic organisms to function is because anaerobic bacteria produced enough oxygen as a waste product to change the composition of gases in the atmosphere. Humans exist only because those tiny creatures performed their functions.
Why is it not possible that bacteria could alter soil pH? They altered the atmosphere of this planet. Why not soil?
Consider the real world, not a greenhouse or lab soil. Nitrate doesn’t exist in soil without the biology present and functioning. Without the organisms to alter the form of N, plants won’t grow. Now, when people add ammonium to the soil, they alter the normal flow of nutrient cycling. When people say plants take up ammonium, what you need to say back, right away, is, “But is that the form of N that will keep that plant healthy?”
What form of N do different plants need? Some scientists say that N is N, it doesn’t matter where it came from. Could that possibly be true? Think about yourself. What form of N do you need? What if you consumed your N in the form of nitrate? You’d be dead in a very short time because your kidneys would go into failure. If you didn’t consume enough nitrate to kill you that way, you’d starve to death. People can take up nitrate, but it will kill us. Is the form of N important? Can people consume ammonia? You’ll die even faster if you try that form of N.
Is the form of N important? Of course it is. Plants have similar requirements. If all you give a plant is nitrate, it will take up nitrate. But is that the correct form for that plant to grow without stress?
If the only thing you give your plant is ammonium, will that plant take-up that form of N? Yes, but is the plant growing in a healthy fashion? If the plant now needs fungicides, insecticides, herbicides, etc in order to grow, this is not healthy. All inorganic N is highly leachable. Stop destroying water quality by putting these leachable forms of N in your soil or potting mixes.
Some plants do best taking up nitrate, others do better with ammonium.
Is there a generalization we can use to say what kinds of plants do best with the different kinds of N? Annual plants, in general, do better with nitrate. Perennial plants do best with ammonium. “Do best” means not stressed, less subject to disease, stronger cell walls, higher production. Annual plants can use ammonium, for example, but they are not healthy, and require much more pesticide in order to stay alive.
Nitrifying bacteria produce nitrate which is the preferred form of N for annual plants in normal soil – no inorganic fertilizer applications needed. Nitrifying bacteria require and maintain alkaline conditions. That means that terrestrial annual plants grow best in alkaline soils. And they do, in general.
The form of nitrogen is very important then, is it not? When bacteria and fungi grow in the soil, what form of N are they taking up? They probably prefer protein, but they will also take up nitrate, nitrite and ammonium – all of the inorganic forms of N can be taken up by these organisms. But not all species use all kinds of N. Presence of high concentrations of NO3 will select for certain communities of bacteria, or fungi. Nitrite selects for other species, ammonium for other species.
Look at a picture of the root of an annual plant taken with a microscope. In the book called “The Ultrastructure of the Root”, by R. Fosterm the most noticeable thing you will see is the deep layer of “slime” present on root surfaces, and the soil around the root. Everything is embedded in the slime produced by bacteria.
Recent work from the USDA in Beltsville show that mycorrhizal fungi also produce significant glues to hold the fungal hyphae on the root, and which help form macro-aggregates in the soil. The pH of these glues are alkaline. When we deal with row crop plants, with most mid-to-early successional grasses, with most terrestrial weeds, and most early successional terrestrial plants, the pH around the roots is alkaline.
But given that the slime layer, the glue around aerobic bacterial cells is alkaline, and there are millions of bacteria per gram of healthy soil, they have to have a large role in influencing soil pH, especially if the soil is bacterial-dominated.
Don’t over-extrapolate to wetland plants, riparian plants, hydroponic situations, or high production ag conditions. Different things are going on there. Think about the fact that most plants in high production ag fields are extremely sick, very stressed, and not functioning normally. If they were healthy, they wouldn’t need all those pesticides, and they would be able to establish and out-compete the weeds. So, any example based on conventional ag cannot be used. Seriously different things are going on there. And pH is being jerked around all the time by high lime, or gypsum or anhydrous ammonia, or other additions.
Humans alter pH with very little effort. So, you can’t use pH as a meaningful measure of anything if pesticides, high level of fertilizers, or compaction have been imposed on soil. And what intensive agricultural soil has not had pesticide, herbicide, high levels of inorganic fertilizer, and severe compaction imposed on it?
But how can normal soils have lower pH than neutral? Different organism dominance. Fungi produce organic acids as major components of their metabolism, but not the STRONGLY acidic organic acids that occur in anaerobic conditions. So, when we test soils that are aerobic, and fungal-dominated, the pH is always somewhere between 5.5 and 7.
This means the nitrifying bacteria are not major players in converting ammonium to nitrate, and so ammonium stays ammonium in fungal-dominated, pH 5.5 to 7.0, healthy forest soils.
What happens in compacted soils?
Compaction destroys the air passageways and water infiltration hallways in soil. If possible, the aerobic organisms start re-building the structure immediately, but their activities may use up the oxygen faster than oxygen can diffuse into the soil. When that happens, the soil loses oxygen, and may move into the facultative anaerobic and finally into the anaerobic zone of metabolism.
How rapid is the loss of oxygen? Depends on how active the organisms are, and how limited the diffusion of oxygen into the soil. Do a soil penetrometer reading. Look how far down the roots of your plants grow.
Take a look at some of Steiner’s and Pfiffer’s drawings of how far down roots went into soil just a mere 50 or 60 years ago. And now look at what current soils books tell you about root depth.
Something has happened. Roots of plants today don’t seem to go down as far as they used to go down.
Look at the USDA definition of soil depth. In the 1940-s and 1950’s, soil was defined as material in which you can grow plants. That depth was determined by how far down roots went, and in the 1930’s, that depth was defined as 4 to 6 inches. In the mid-1980’s, soil depth was re-defined as going down to 12 to 18 inches. In 1994, soil was re-defined again as going down 4 ft. Below those zones, in any time period, you could not get plants to grow in ag that soil. Except for tap roots, roots would not grow deeper than those depths.
How can that be? You have to understand tillage equipment. In agriculture, up to the 1970’s, most soils, especially in the Midwest were tilled with mold-board plows which turn the soil to a depth of 4 to 6 inches. With continuing tillage, the soil became so compacted at that depth that water and air could not move through it. The “soil” below that point was anaerobic, salt problems occurred. Water would hold up and not penetrate further into the soil. In the spring, that pan would prevent water from moving into the soil, and then erosion occurred, taking soil downhill.
The solution to this was an engineering approach. Have a hard pan? Break it open physically. Plow deeper. Chisel and disc plows go down to, 12 to 18 inches. The hardpan at 4 to 6 inches was broken up, but the compaction zone was then imposed at 12 to 18 inches, depending on your equipment. Within a few years, the hardpan was so bad at those depths that deeper tilling equipment was invented. We need to break open the compaction zone at 12 to 18 inches, by deep-tilling, or sub-soiling. We shatter the soil down to 4 feet, and so we develop two compaction zones. One at 4 feet, and the “normal” ones at 12 to 18 inches.
As compaction occurs, oxygen movement slows, aerobic organisms go to sleep. Anaerobic organisms start to grow. In aerobic conditions, the bacteria making alkaline slime were predominant. But as anaerobic bacteria, and yeasts (which are fungi, but are not normally functional in soil in aerobic conditions), begin to win in competition with aerobes for the food resources.
Consider the metabolites produced in anaerobic conditions. Alcohols are a major component of anaerobic conditions and are among the most phytotoxic materials that we know. In anaerobic conditions, the roots will be killed.
Unless it’s a riparian or wetland plant. Then these roots have mechanisms for dealing with and getting rid of alcohol. They have the plant world’s equivalent of livers. Enzymes are produced which destroy alcohol, or they pump oxygen into the root system, for example.
What else is produced in anaerobic conditions? Some very toxic organic acids, such as acetic acid, proprionic acid, butyric acid, valeric acid, and a host of other low pH organic acids, only produced in anaerobic conditions. So, what happens to soil in anaerobic conditions? The pH can fall into very low levels. These severely low pH organic acids are strictly produced by anaerobic organisms, and become the dominant determinant of soil pH when the whole soil profile, or a major part of the soil, becomes anaerobic.
Some really nasty phenols are also produced under anaerobic conditions. More killing power in these anaerobic conditions.
What happens to ammonium, or nitrate in anaerobic conditions? They are lost as volatile gas, ammonia. Ammonia is a product of anaerobic microbial metabolism. What happens to sulfur in anaerobic conditions? Lost as hydrogen sulfide. What happens to phosphate in anaerobic conditions? Lost as phosphine gas. Can’t smell it, but you can see it. The anaerobic organic acids metioned above, and of course ammonia and hydrogen sulfide, you can smell. If it stinks, there’s anaerobic metabolism occurring.
Can you grow plants in something where N, P, S has been lost, or at least significantly reduced? Certainly not going to grow well.
Will you be able to grow healthy plants in something where plant-toxic materials have been produced?
Can you grow plants in something where the nutrient-cycling organisms have been killed, or at least put-to-sleep by the lack of oxygen, to say nothing of the toxic effect of alcohol, low pH organic acids, and phenols, or the loss of the exudates from the root systems?
So, at low pH, the soil is in serious trouble. Below pH 4.5, terrestrial plants are not going to do well. Riparian plants? Wetland plants – different story, as explained above.
So, closing the nitrogen cycle requires anaerobic conditions, which results in nitrate or ammonium being blown off as a gas, ammonia, nitrous oxide, or nitrogen gas. And nitrogen is back where we started – in the atmosphere, where our biggest reserve of N is.
Please see the books and CD’s by Dr. Elaine Ingham to hear more about the N cycle, microorganisms, and plant growth.
