Throwing a wrench in biogeochemical cycles

Water Cycle USGS“Biogeochemical cycles” used to be a phrase that sent me running for the coffee. I know that understanding biogeochemical cycles will make me a better ecologist, and that biogeochemical cycles are fundamental for getting the big picture. Unfortunately, every time I tried to learn more about the subject, I ended up getting lost and bored in the seemingly endless web of arrows and equations. A particularly good ecology class, however, started to change that. When we got to the section on biogeochemical cycles, I braced for another dull series of lectures on nitrogen mineralization. But it turns out, biogeochemical cycles aren’t nearly so boring to me when humans are included in the equation.

But let’s back up a second. What exactly is a biogeochemical cycle? A biogeochemical cycle describes how chemicals like nitrogen and water move through and between the ground, water, air, and living things. A good example of a biogeochemical cycle that the average middle schooler is familiar with is the water cycle. But I want to tell you about the carbon and nitrogen cycles and what people have to do with these planet-sized processes.

This continues a series inspired by a 2001 paper by Novacek and Cleland. Other posts are

The carbon cycle

Because of all the news on carbon dioxide and climate change, you’re probably more familiar with this cycle than you think. This infographic gives a pretty good summary of the cycle:

Carbon cycleYou can think of carbon as being stored in a few big ‘pools:’

Carbon is stored in many different chemical forms. Carbon in fossil fuels, for example, might be locked away underground as methane or cyclobutane. Carbon in sea shells is bound up with calcium. We’re little carbon storage units, too: almost 10% of the atoms in our bodies are carbon – everything from our fatty acids to our DNA has carbon. Carbon moves naturally between the pools through processes like photosynthesis (atmosphere -> plants), respiration (living things -> atmosphere), or volcanoes.

People and the carbon cycle

Humans change the balance of carbon in each pool in many different ways. Burning forests move carbon from the trees to the atmosphere. Planting trees moves carbon from the atmosphere to the growing trees. Some agricultural methods lead to lots of carbon storage in the soil, while other methods cause lots of carbon to move back to the atmosphere. Burning fossil fuels moves incredible amounts of carbon from deep underground into the atmosphere. That last one is in large part responsible for climate change. Ten years ago, Cleland and Novacek had this to say:

Some suggest that the effects of climate change on the current biota are already observable in the terms of physiology, distribution, and phenology (27). For example, warming of the oceans could seriously impact on the convergence of warm water and cold water that is responsible for the nutrient-rich upwelling in the Southern Ocean off the coast of Antarctica. This change in current regimes could in turn reduce one of the sea’s main staples: krill. These organisms account for about 250 million tons of food for whales, fish, seals, and other species annually, more than two and half times the annual yield of the world’s fisheries (22).

Now, we’re seeing phytoplankton/krill in decline. And that isn’t the only climate change prediction to come true. Phenology (biological timing – when flowers bloom, when birds lay their eggs, etc.) is changing quickly and in some cases species are getting out of sync. Where species can live is also changing rapidly, leaving scientists scrambling to develop and perfect modeling methods that can tell us what’s going to be left.

We’re pushing so much carbon into the atmosphere that it can’t hold it all and so carbon dioxide gets pushed into the oceans – like making a salty soda. This creates a whole bunch of other problems because adding carbon dioxide to the ocean makes it more acidic. That’s as bad for fish as it sounds.

So we’ve thrown the carbon cycle all out of whack by moving carbon buried in the ground or stored away in plants to the atmosphere and the ocean. And that’s the cause of climate change in a nutshell. But the carbon cycle isn’t the only biogeochemical cycle we’ve thrown a wrench into.

The nitrogen cycle

Nitrogen is absolutely essential for life on earth – all living things need nitrogen to build proteins. There’s a whole lot of nitrogen, mostly in the air. Even though it’s all around us, it’s hard for many living things, like plants, to get enough. How can that be?

Well, like carbon, nitrogen can be found in a lot of forms. And plants can’t use the most common forms. There are 5 main steps for how nitrogen moves between soil and air and living things. (This is the part where I usually grab more coffee. Good luck!)

Fixation. In the atmosphere, nitrogen is found as two nitrogens bonded together. Most living things can’t use this atmospheric nitrogen. But special bacteria can! These bacteria “fix” the atmospheric nitrogen, changing it into a form that plants can use. (Very cool fact: lightning does this too!)

Assimilation. Once the nitrogen is “fixed,” plants can assimilate it. That is, plants take up the ‘fixed’ nitrogen and use it to make enzymes and defensive compounds and all sorts of other stuff they need. The nitrogen in plants is the source of all nitrogen found in animals – including you.

Ammonification/Mineralization. When plants and animals die decomposers change the available nitrogen in our/their bodies into ammonium, which plants and animals can’t use.

Nitrification. Then certain bacteria convert the ammonium into nitrites and then nitrates. This is an interesting step because a whole lot can happen from here. Nitrates can be used by plants, but they’re also soluble in water. So if it rains, the nitrogen can leach out of the soil into groundwater and streams. If plants use it, we’re back to the assimilation step.

Denitrification. Other bacteria can take the nitrates from the previous step and turn them back into atmospheric nitrogen. Then we’ve got to start over with fixation.

Here’s a nice summary of the whole process:

The Nitrogen Cycle from Wikimedia

But that’s all on land. In the oceans, one of the most important processes is called anammox, short for anaerobic ammonium oxidation. In annammox, the cycle gets short circuited after ammonification and the first part of nitrification – instead of getting nitrates which lots of living things can use, the ammonium and nitrite are coverted straight back into atmospheric nitrogen.

People and the nitrogen cycle

We haven’t doubled the amount of carbon in the atmosphere (yet…), but we have doubled the amount of nitrogen moving through the nitrogen cycle. Almost all of our impact on the nitrogen cycle is through fertilizer manufacture and use. Remember the fixation step in the nitrogen cycle? Only a few special bacteria can turn atmospheric nitrogen into a form other living things can use. But, through the power of chemistry, people have also figured out how do what bacteria do, turning atmospheric nitrogen into plant available nitrogen (and also nitroglycerin).

If bacteria were still running the show, our soil and water would have half the amount of nitrogen it does now. You might argue all that extra nitrogen is a good thing – I’m not sure it’s possible to support our huge human population without all the fertilizer we use. But there are some pretty nasty effects of adding all that extra nitrogen to our soil and water. Novacek and Cleland summarize the problem in understated science-ese:

Human activity has essentially doubled the amount of nitrogen cycled globally (28), contributing to nitrogen sinks in soils, surface waters and deep oceans, and the atmosphere, and this increase has detrimental effects on biodiversity and ecosystem function.

Whale killed by harmful algal bloom. Algal blooms are often caused by an influx of nitrogen and other nutrients from our farms and wastewater.

This is a whale killed by conditions created by an algal bloom – either toxins or a lack of oxygen from the algae. In the grand scheme of things, the death of a couple whales is sad, but not a big deal. But the number of dead zones we’ve created is most definitely a big deal. Dead zones are areas in our lakes and oceans where almost nothing can survive. And they’re caused by fertilizer.

How on earth does fertilizer far inland lead to huge areas in the ocean where nearly nothing can live? Remember the nitrification step in the nitrogen cycle? At the end of that step nitrogen is in a form that dissolves in water. When people interfere in the nitrogen cycle and make nitrogen fertilizer, we usually apply it in this water soluble form. Whatever the plants don’t immediately suck up leaches out of the soil and into streams and rivers and, eventually, the ocean. Notice how many of those red dots are at river mouths.

Dead zones: "Red circles on this map show the location and size of many of our planet’s dead zones. Black dots show where dead zones have been observed, but their size is unknown. It’s no coincidence that dead zones occur downriver of places where human population density is high (darkest brown). Darker blues in this image show higher concentrations of particulate organic matter, an indication of the overly fertile waters that can culminate in dead zones."


Burning fossil fuels is another way we alter the nitrogen cycle with negative consequences for ourselves. You’d be wrong if you thought burning fossil fuels was all about carbon. Your car and thermal power plants belch various nitrogen oxides. Even if you didn’t know that little bit of chemistry, you certainly know what happens when those nitrogen oxides meet clouds:

Forest damaged by acid rain. By Getty Images on The Discovery Channel.

Moving the weights on the levers in our our biogeochemical cycles changes how our world works in ways that are really bad for us. Novacek and Cleland pinned their hopes for getting the carbon cycle back under control on the Kyoto Protocol, which is dead in the water. And I don’t think we’ll see another significant step towards getting climate change under control until businesses are seeing clear, immediate, and dramatic effects on their profits. Getting the nitrogen cycle back to normal requires a serious commitment to anti-pollution efforts and reduced use of fertilizer.While the EPA is working on nitrogen, we’ve still got a long way to go.

Restoring the balance to our biogeochemical cycles won’t be easy, but it will be easier than living in a world ravaged by climate change, dead water, and acid rain.

Novacek, M., & Cleland, E. (2001). The current biodiversity extinction event: Scenarios for mitigation and recovery Proceedings of the National Academy of Sciences, 98 (10), 5466-5470 DOI: 10.1073/pnas.091093698