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Soil Science: From the Textbook to the Practical. Nitrogen part 2. The Nitrogen Cycle: Pools, leaks and wallets full of nitrate

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This article comes from the NOFA/Massachusetts 2019 June Issue Newsletter

By Noah Courser-Kellerman for NOFA/Mass

In the previous installment, we delved into what nitrogen is, why plants need it and how plants, bacteria and humans get it.  Today we will delve into how it moves through our farms and interacts with global systems. The concept of a biogeochemical cycle is useful in thinking about how elements behave on a micro and global scale. As can be seen in the roots of the word, a biogeochemical cycle involves biological, from organism to ecosystem, and abiotic systems such as the atmosphere. It makes sense, on a planet whose continents appear green from photosynthetic organisms from space, that life is a driving force inextricable from chemical and geological processes. Humans, of course, need to come to terms with this reality. We cannot live on the planet without changing the planet, and the kind of planet we will have to live on will be the direct result of our actions.  Other examples of biogeochemical cycles are those for water, carbon and sulfur.

Pools and the Nitrogen Economy:

It is useful to think of each stage of a biogeochemical cycle in terms of “pools.” Each form of nitrogen takes in an environment is a pool. Like interconnected puddles, there is constant flux, with nitrogen flowing from one to the other, changing forms.

Nitrogen is only available to plants (and by extension, to humans) in a few pools of the cycle in the soil. At each stage in the soil ecosystem, some nitrogen is recycled, to be used again by other organisms in the soil, and some is lost to the atmosphere or water. Keep an eye on this “loss” at each stage of the cycle: the amount and type of loss is what determines the efficiency and amount of environmental damage incurred by our farms’ role in the N cycle.

The three main pools of nitrogen in the soil are inorganic N, biomass and Soil Organic Matter (SOM). Ammonium and Nitrate in the soil are the inorganic (non carbon-containing) pool. These are constantly being used by living organisms, and thus enter the next pool: biomass. Organisms die or excrete nitrogenous waste, and this biomass N is “mineralized”—released back into the first pool as inorganic ammonium again. Soil organic matter, the third pool, is dead biomass that hasn’t been mineralized yet through decomposition by bacteria and other organisms. Nitrogen passes between these three pools as organisms like roots, fungi, earthworms and bacteria grow, die and decompose in the soil.

Nitrogen pools in the soil and money in an economy flow in similar ways. I like to think of inorganic nitrogen as cash. Biomass and SOM nitrogen can be thought of as bank accounts and property. Cash can buy things, or be stored in a bank account, much as inorganic nitrogen can be used by living things or be stored in the tissues of living organisms or as SOM. Biomass and SOM can be decomposed, releasing inorganic nitrogen, just as cash can be withdrawn from a bank account and property can be sold for cash.

A tight nitrogen cycle, featuring Buttercup, the Cow.

"Buttercup" the cow lives on pasture on an organic dairy farm in New EnglandEven though the N cycle is global, we can follow its stages on a very local scale, say on an organic dairy farm in New England, where a herd of Jerseys munch green grass, lounge around and live their bovine lives. Let’s follow nitrogen as it moves from air to plant to cow to soil ecosystem and back again.

Most N, as we discussed earlier, is in the form of dinitrogen, N2 and makes up almost 80% of the air we breathe. N2 from the atmosphere passes through the wall of an earthworm burrow in the pasture, and into the root nodule of a clover plant. Rhizobia bacteria in the nodule use nitrogenase to convert N2 to two NH4+. This Ammonium passes into the clover plant’s sap, and is converted into amino acids, DNA and chlorophyll in the clover’s leaf. Nitrogen has moved from the atmospheric pool into the biomass pool of the soil.

Buttercup, the cow, comes along and eats the clover. Some of the nitrogen in the clover is absorbed through her rumen into her bloodstream, and is rearranged into casein milk protein in the udder and ended up in your mug of coffee this morning. Some of the amino acids are used for energy by Buttercup. Protein leaving the farm as milk is the first “loss” of N from the farm’s nitrogen cycle.

Back on pasture after morning milking, she hunches up and pees. Nitrogen in the form of urea, CH4N2O, soaks into the sod. In the soil, urease enzymes secreted by certain soil bacteria break urea into CO2 and NH3, or ammonia. Some ammonia volatilizes from the soil and goes into the atmosphere. Volatilization is the next “loss” in the system. The rest quickly converts to NH4+, ammonium in the soil. Some ammonium is immediately taken up by the grass roots to be used in protein synthesis to start the process over again.  But plants aren’t the only soil residents interested in Buttercup’s pee.

Bacteria and fungi can use inorganic nitrogen—ammonium or nitrate—in the same way plants can. In most soils, carbon is more abundant than N, so N is the limiting nutrient. With the addition of inorganic N to the soil, bacteria can rapidly multiply to take advantage of the carbon sources they previously couldn’t use.

The nitrifying bacteria go a step further, which is where we get into the strange world of microbial metabolism.  Two forms of metabolism are familiar to most people: Humans, which get energy from breaking the chemical bonds of the food we eat and use organic carbon from food to build our cells are chemo-organo-heterotrophs.  Plants, which get energy from the sun and use inorganic carbon (CO2) to build their cells, are photo-autotrophs. So-called nitrifying bacteria, however, get their energy by oxidizing ammonium, NH4+, which leaves nitrate, NO3-, as a byproduct. These bacteria use CO2 as a carbon source, like plants. They are chemo-litho-autotrophs. Nitrifying bacteria need oxygen to function, so only function when the soil is aerobic. Nitrate can be lost from the soil by leaching more easily than ammonium, representing another “loss” to the cycle.

Hurricane season rolls around, and Buttercup and her herd mates are brought to the barn for shelter.  Three inches of rain fall over twenty-four hours, and puddles appear all over the pasture. Earthworm burrows, the ventilation shafts of the underground city of soil organisms, fill with water, and the oxygen level in the saturated soil falls. Some of the small amount of nitrate—the “cash” in the soil N economy that happens to be in flux in the soil—leaches downward into the groundwater, and some runs off into a nearby creek. This is lost to the system. Some nitrate stays in the soil.

As the soil becomes more and more anaerobic, the nitrate remaining in the soil starts to seem like a pretty good substitute for oxygen for another group of bacteria with a bizarre metabolism referred to as the denitrifiers. These bacteria eat carbon-containing molecules, just like we do, but they use nitrate, NO3,-as the final electron receptor in their metabolism—basically, they breathe nitrate.  Nitrate is a good oxidizer—this is why gunpowder burns without air, and fertilizer is used as an explosive and vice versa—but using it doesn’t return quite as much energy to the bacteria as metabolism using O2 as an oxidizer would.

Denitrification is a process that takes place in several steps and is carried out by several different species of bacteria. Nitrate is disassembled first to Nitrite, NO2-, then NO, Nitric Oxide, to N2O, Nitrous Oxide, or laughing gas, and finally back to dinitrogen, N2. Denitrification is another loss of N from the cycle. The N2 goes back into the air, and the cycle can begin again. At least, that’s the way it’s supposed to work.

If the process is interrupted—if the soil dries out and oxygen comes back into the soil, or if winter comes too early and it gets too cold for the last crew of denitrifiers to finish the job, Nitric and Nitrous Oxide will escape into the air. Far from the hilarity of a loopy drill session at the dentist, this is a real problem. Nitric oxide is a major contributor to smog and acid rain. Nitrous oxide is a potent greenhouse gas: a molecule of N2O stays in the atmosphere for over a century, on average, and has a heat trapping potential of nearly 300 times that of CO2! Globally, cropland is the biggest human-caused source for N2O emissions.

It’s worth noting that all of the loss of N from Buttercup’s pasture (except from milk and beef leaving the farm) has been in inorganic form. Ammonia can volatilize and waft away before turning to ammonium, which is then converted into nitrate by nitrifying bacteria. Nitrate can leach from the soil or can be converted to nitrous oxide or N2 by denitrifying bacteria when the soil becomes anaerobic. Meanwhile, N in the biomass and SOM pools in the soil is relatively stable. Thankfully, in the well-developed sod of Buttercup’s pasture, the vibrant community of roots and microbes in the soil quickly snatch up most of the inorganic nitrogen and safely hold it as biomass or SOM. At any given time, there is comparatively little nitrate or ammonium in the soil. This results in a relatively small amount of “leakage” from the nitrogen cycle.

Seen through the analogy of inorganic N as cash, this makes sense. The more N in the inorganic pool, the more vulnerable to loss it is, just as the more cash I carry, the more vulnerable I am to theft or loss. The biomass and SOM pools, analogous to bank accounts and real property, are the safe way to store N in the soil.

The “leaks” in the nitrogen cycle on Buttercup’s farm are found on virtually every farm and garden. The size of leak, however, varies greatly. Management, crop choice and tillage, the application rate, timing and choice of nitrogen fertilizers, and soil health has a huge impact on how tight nitrogen cycling on any piece of land will be. Some farms, like Buttercup’s, represent the organic ideal, where so little nitrogen is lost from the farm that nitrogen fixation by legumes and free living nitrogen fixers (and the odd lighting strike) more than make up for leaks in the system and milk and beef leaving the farm. On farms where losses of N exceed fixation, fertilizer becomes necessary to maintain production.

A leaky nitrogen cycle, featuring Bessie, the cow.

"Bessie" the cow lives in a barn on a conventional dairy farm in New EnglandShamefully low commodity prices paid to conventional dairy farmers in New England and comparatively cheap fuel and fertilizers have allowed a leaky nitrogen cycle to develop on many farms. One of the biggest differences between many conventionally managed dairies and organically managed ones is that conventionally managed cows typically have little or no access to pasture, even during the growing season. Feed is brought to cows in the barn, and their manure is stored and then spread. Organically managed cows still live in a barn during the winter, but are required to be pastured for as much of the year as possible. Manure management is different too. A typical conventional dairy manages manure as a liquid, storing it in tanks and spreading the slurry on their land. Many organic farms use large amounts of bedding like straw or sawdust to soak up manure and urine, and either spread the bedding/manure pack or compost it to create a more stable product. Most conventional farms rely on annual crops like corn for silage to produce an energy-dense feed to keep milk production high.

Bessie, a big Holstein from a conventional confinement dairy farm looks up from the feed bunk brimming with silage and alfalfa and takes a big pee. Her urine mixes with the urine and manure from her neighbors, and a few hours later is scraped into the manure storage pit. All the while, bacteria and their enzymes convert urea to ammonia. This is the first big leak in Bessie’s farm’s nitrogen cycle. Because her waste is not mixed with a high carbon bedding material, where bacteria might incorporate nitrogen into their tissues, the inorganic ammonia is free to evaporate.  A mentor of mine put it this way: The smell of ammonia is the smell of dollars leaving your farm.

In the layer of the pit that is exposed to air, ammonium is converted by nitrifying bacteria to nitrate. As that nitrate diffuses to the layers of the pit where all oxygen has been used up, the denitrifying bacteria breathe the nitrate and nitric oxide, nitrous oxide and dinitrogen waft away into the atmosphere. This denitrification represents the next leak in the system. Meanwhile, in the anaerobic depths of the manure pit, methane generating bacteria ferment the carbon in the manure, generating gas that, if not captured and burned as fuel, contributes to climate change at a much higher rate than CO2. From a nitrogen perspective, this loss of carbon is important because the less carbon there is, the more of the manure’s nitrogen will be in inorganic form, making a saltier, stinkier, more volatile slurry than the original manure.

In the spring, the manure pit’s contents are spread on the corn ground. The few earthworms in the soil writhe to the surface as the caustic slurry pours down their burrows, where they are slurped down by a flock of seagulls following the spreader. Bessie’s farm has been growing silage corn without tillage for a number of years. Manure is applied, seeds that can withstand glyphosate are planted, and Roundup is used to keep weeds down through the growing season. Even though the farm is on a beautiful river valley loam, years of chemicals, a history of tillage, annual crops and huge equipment have compacted the soil. More ammonia wafts away, and nitrifying bacteria have a field day converting the remaining ammonium in the soil into nitrate. Planting is delayed for a week while a rainstorm passes and the soil dries out. Because the soil is compacted and there are few earthworm burrows or pore spaces, the soil stays saturated for a few days. During this time, more nitrogen is lost to nitrate leaching to the river, and to denitrification as oxygen levels fall in the saturated soil.

Because there is little SOM and no living roots in the soil, most nitrogen from the manure that was in an inorganic form at application has stayed in the inorganic pool or has been lost. At one time in this field, there was more SOM. The soil was darker in color, softer, and held water. The SOM also acted like a sponge for nitrogen.  During the summer, the organic matter in the soil partly decomposed, releasing CO2 and nitrogen for the crop. Cover crops, manure mixed with bedding and a rotation between corn and alfalfa balanced nitrogen and carbon withdrawal from the SOM bank with deposits. When nitrogen in inorganic form began to be added at greater rates, bacteria, no longer limited by nitrogen, began to consume the organic matter of the soil to meet their carbon needs.  Over time, the soil’s capacity to hold and protect nitrogen—a bank for all that cash—was diminished, in part, by the excessive use of nitrogen. A soil with much of the N needed for that year’s crop in inorganic form is like a household in which the breadwinner’s salary for the coming year is strewn all over the floor in one dollar bills. This is a vulnerable situation.

Finally, seeds go in the ground and the weather improves. The corn takes off, and the gray-brown soil of the field disappears under a rustling dark green canopy of corn. Before the corn gets too tall to get a tractor in the field, the human from Bessie’s farm takes a pre-side dress nitrate test, or PSNT, to figure out if there is enough nitrogen in the soil for the corn crop to continue to grow well for the rest of the season. The rule of thumb is that if there are 25 parts per million of nitrate in the soil, there is enough nitrogen for the crop. Because of the losses from the rainstorm earlier in the spring, and the diminished state of the SOM nitrogen bank, the test comes back showing that the crop will be short on nitrogen. The farmer applies a dose of synthetic urea, to see her crop through. Because the fertilizer can volatilize as it sits on the soil surface, the farmer broadcasts the fertilizer just as a thunderstorm approaches so that the granules will dissolve and wash into the soil. Unfortunately, the thunderstorm fizzles before it reaches the cornfield, and more nitrogen goes back into the atmosphere before the corn can get it.

The corn finishes well and is chopped at the end of September for silage. Only a portion of the nitrogen applied to the soil made it into the corn now fermenting in a trench silo. Even though the corn is no longer growing, organisms in the soil are still eating each other and organic matter, and mineralizing nitrogen. The nitrate level in the cornfield’s soil in September is as high as it’s been all season, and spikes as the corn stops soaking it up. The farmer knows that a cover crop of winter rye might save twenty or thirty pounds (15-25% of the crop’s needs) per acre of nitrogen for next year but between getting all the corn chopped, the cows milked, the kids taken care of, and getting the barn roof fixed before winter, it just doesn’t get done. As the soil cools, and fall rains saturate the soil again, more nitrate leaches or is denitrified. Come spring, there is little inorganic nitrogen remaining in the soil, and the cycle begins again.

This vignette is not meant as a critical comparison of organic vs. conventional. There are superbly managed conventional dairies, and even the best organic dairies lose nitrogen in the same ways as the field where Bessie’s silage grows. I personally know an organic dairy run by two of the most conscientious farmers out there, whose well became contaminated with nitrate leaching from their composting site during a rainy summer.  Organic manure often stinks just as bad as everyone else’s. Most organic vegetable farms have more in common with Bessie’s cornfield than Buttercup’s pasture.

Instead, I hope to have illustrated that as farmers and gardeners, each management decision we make can have a big impact on how leaky or tight our nitrogen cycles can be.

The bigger picture: The human and environmental impact of Nitrogen Leaks

The nitrogen lost on these and many other farms contributes to myriad environmental and public health problems, from blue baby syndrome caused by nitrates in groundwater, to dead zones where rivers spew contaminated water into rivers and lakes, to smog and, perhaps most dire, climate change. In addition to nitrous oxide’s role in climate change, the manufacturing of synthetic nitrogen itself uses vast amounts of fossil fuels. To manufacture the nitrogen fertilizer needed for an acre of field corn takes the equivalent of over 13 gallons of diesel fuel, far more than is used plowing, planting, spraying and harvesting combined. 

As farmers and environmentalists we need to begin to think about nitrogen inputs (organic or otherwise) the way many of us have come to think of gasoline: It is a precious, powerful resource, but we know it causes problems in the world. We first try to find ways of getting around without it, then we try to drive vehicles that use it efficiency, and most of all, we try not to waste it.

In the next installment, we will delve into practical management of nitrogen with the goal of making a tight nitrogen cycle on our farms, including organic fertilizers, cover crops, timing and tillage. I will focus on vegetable production, but as with Buttercup and Bessie’s farms illustrate, the principles apply to other types of farming as well.

Find the rest of this e-mini series “Soil Science: From the Textbook to the Practical” on the NOFA/Mass website in our newsletters from January 2019-June 2019.

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