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The NPR article and 4 minute audio news item Can Anyone, Even Walmart, Stem The Heat-Trapping Flood Of Nitrogen On Farms? discusses unexpected contributions of greenhouse gasses from the manufacture of consumer goods. One example is bread, or agricultural products in general, and part of this is the anhydrous ammonia used in fertilizer.

Carbon dioxide seems to be a bi-product of the manufacture, but nitrous oxide a more potent greenhouse gas is produced by bacteria in the soil as a result of application of ammonia.

Manufacturing nitrogen fertilizer is energy-intensive, burning lots of fossil fuels and releasing carbon dioxide. What's just as damaging, and perhaps even more so, is what happens when it's spread on a field. Bacteria feed on it and release a super-powerful greenhouse gas called nitrous oxide.

These bacteria are naturally present in the soil, says Philip Robertson, a researcher at Michigan State University, "but once they get exposed to nitrogen fertilizer, they really light up" and pump out nitrous oxide.

Question: Is it common for most soil bacteria to make significant quantities of nitrous oxide after ammonia is added, or is there only a small subset of bacteria present in soil that might do this? Also, what is the metabolic pathway in this case? Is this a waste product from "eating" ammonia, or something more complicated/subtle?


below: Anhydrous ammonia tanks in a newly planted wheat field. Walmart has promised big cuts in emissions of greenhouse gases. To meet that goal, though, the giant retailer may have to persuade farmers to use less fertilizer. It won't be easy. TheBusman/Getty Images. From here.

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    $\begingroup$ This is just a step in the nitrogen cycle, called nitrification. It's performed by chemoautotrophic prokaryotes that obtain energy oxidising ammonia to NO. So, answering your questions: 1. no, only very specific species do that. 2. It is a waste product for that given species, but NO will be subsequently metabolised by other species. $\endgroup$ – user24284 Aug 23 '17 at 3:49
  • $\begingroup$ @GerardoFurtado I see, but my question is about nitrous oxide N${}_2$O and not nitric oxide NO. $\endgroup$ – uhoh Aug 23 '17 at 4:10
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    $\begingroup$ Thanks, but I'm a bit busy now and here at BioSE if you don't write a thesis with 5 chapters, references and acknowledgements you get some downvotes. Just wait some time and someone else will write a proper answer. $\endgroup$ – user24284 Aug 23 '17 at 4:14
  • $\begingroup$ @GerardoFurtado I understand what you mean - thanks! Also I've just changed my comment above - sorry about that. $\endgroup$ – uhoh Aug 23 '17 at 4:15
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    $\begingroup$ My bad, in my mind I read "nitric oxide". Mmm, if you're talking about N2O things are more complex, because it is produced both in nitrification and in denitrification: ncbi.nlm.nih.gov/pmc/articles/PMC5016788. See this: "The emission of N2O is the result of multiple biological pathways, such as nitrification (autotrophic and heterotrophic), denitrification, dissimilatory nitrate reduction to ammonium (DNRA), nitrifer denitrification, and non-biological chemodenitrification". $\endgroup$ – user24284 Aug 23 '17 at 4:17
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Addressing the first part of your question:

Is it common for most soil bacteria to make significant quantities of nitrous oxide after ammonia is added, or is there only a small subset of bacteria present in soil that might do this?

No, not all soil bacteria can oxidize ammonia. According to wiki:

The oxidation of ammonia into nitrite is performed by two groups of organisms, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA).

The role of archaea in the soil nitrogen cycle is not well-known yet, although it could be greater than that of bacteria. On the other hand, the role and metabolism of AOB are more or less studied.

The process of ammonia-oxidizing is also called nitrification and AOB sometimes referred as nitrifying bacteria. The most known bacteria genera from this group are Methylomonas, Nitrosococcus, Nitrosomonas and Nitrosospira. I think the most studied species is Nitrosomonas europaea Winogradsky 1892.

For reference see: Arp DJ, Sayavedra-Soto LA, Hommes NG. Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea. Arch. Microbiol. 178 (2002) 250-5.

The second part of the question:

What is the metabolic pathway in this case?

Although, the metabolic pathways vary in different genera, let's look at ammonia metabolism in N. europea.

In the simplest case, it is a two-step process. According to KEGG:

Step 1. The enzyme ammonia monooxygenase converts ammonia to hydroxylamine. The enzyme contains copper, iron and possibly zinc. It requires two electrons, which are derived indirectly from the quinone pool via a membrane-bound donor. The reaction is:

NH3 + a reduced acceptor + O2 = NH2OH + an acceptor + H2O

Step 2. The enzyme hydroxylamine dehydrogenase converts hydroxylamine to nitrite. This reaction requires specialized cytochrome as an acceptor of electrons. The reaction is:

NH2OH + H2O + 4 ferricytochrome c = NO2 + 4 ferrocytochrome c + 5 H+

While nitrite is the main product, the enzyme from N. europaea can produce nitric oxide as well. Therefore Step 2 can produce nitric oxide (NO). In this case, additional mechanisms of converting NO to NO2 are involved.

Further destiny of released nitrite can be different. In one process it could be oxidized by different microorganisms (bacteria, archaea) to nitrate (NO3) which could be consumed by plants or washed out to deeper horizons with water. In another case, nitrite, nitric oxide and nitrate could be involved in process of denitrification. During this process, a group of denitrifying organisms (bacteria, archaea and fungi) consume nitrogenous compounds and reduce them to nitrogen (N2), which can escape to the atmosphere. This process can occur through different metabolic pathways mainly with aid of reductases like nitric oxide reductase. One of the possible intermediate product of such pathways is a nitrous oxide (NO2). If N2O escapes from cells we can observe a resale of nitrous oxide from soil.

Let's return to your first question, and particularly to the part where you ask about significant amounts of nitrous oxide.

First of all, nitrification is a natural process and is a part of the nitrogen cycle. Some organisms fixate nitrogen and convert it to ammonia, some oxidize ammonia to nitrous compounds and some of them reduce it back to nitrogen. It occurs everywhere virtually in all terrestrial and water biocenoses. In a healthy ecosystem, the inflow of nitrogen is theoretically equal to the outflow (with temporal deposition in trophic chains). In such natural conditions, the release of nitrous oxide should be neglectable.

The situation changes significantly when we add an ammonia to soil artificially as a fertilizer. The main problem is that we break an equilibrium between nitrogen fixation, nitrification and denitrification. The second big problem is that an ammonia is toxic for most organisms, so we can alter microbiome. In such case, we can expect an excess of products of nitrification and improper denitrification with exaggerated levels of released nitrous oxide. The actual proportions vary significantly depending on both biotic and abiotic conditions, therefore it is difficult to predict real levels of nitrous oxide released without in situ examination.

P.S. sorry for possible bad writing.

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  • $\begingroup$ Very interesting and informative answer! I will take a closer look in the morning, thank you! $\endgroup$ – uhoh Oct 11 '17 at 17:38
  • $\begingroup$ Well that was quite a long morning! Nonetheless thank you very much for your answer! Just fyi I've asked a related question in Earth Science SE: How can agricultural ammonia lead to PM2.5 production in the atmosphere? $\endgroup$ – uhoh Apr 4 '19 at 1:01
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if I give you a can of anhydrous ammonia, and I drop in a match, it will blow up, yielding nitrous oxides.

it is an exothermic energy releasing reaction.

bacteria figured this out, and use this same chemical reaction, albeit with more steps, to derive their own energy, and therefore drive their own matabolism.

like the way a marshmallow (sugar) will burn, our bodies have figured out how to burn sugar without heat and yield ATP, certain bacteria do the same, but with ammonia. the nitrous oxides are then converted into nitrites by other bacteria, and finally to nitrate by yet other bacteria. And finally, some of the nitrates go into the plants, while others, get turned back into nitrogen, like when bitrate in gunpowder explodes (cool!)

this is called "nitrification" as some people in the comments have said.

google the nitrogen cycle if you havent already. it is very fascinating.

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  • $\begingroup$ Can you be a little more specific than "bacterial have figured this out"? Are you suggesting that they have very recently evolved to do this after the application of anhydrous ammonia became common, or is there enough naturally occurring anhydrous ammonia in the environment that this pathway exists already? Can you also re-read the question (the part explicitly labeled Question:) and address it specifically? Thanks! $\endgroup$ – uhoh Oct 7 '17 at 0:58
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    $\begingroup$ as soon as the ammonia hits the dirt, it stops being anhydrous. also, bacteria have always known how to do this $\endgroup$ – 4D Neuron Oct 8 '17 at 1:33
  • $\begingroup$ OK that's very helpful! Would you consider addressing the question as asked: Question: Is it common for most soil bacteria to make significant quantities of nitrous oxide after ammonia is added, or is there only a small subset of bacteria present in soil that might do this? Also, what is the metabolic pathway in this case? Is this a waste product from "eating" ammonia, or something more complicated/subtle? $\endgroup$ – uhoh Oct 8 '17 at 4:12

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