Welcome to BIO121/ESS120: Introduction to Environmental and Ecological Microbiology at UC Merced! This page provides additional online content associated with the course, including short video lectures by Professor Beman, additional videos and interactives, and additional reading materials.
Microbes, Global Biogeochemical Cycles and Global Change
We’ve learned about microbes in different habitats and how they can generate energy using different redox processes. When we put all of that together, we see that microbes play a central role in Earth’s biogeochemical cycles. These are cycles of essenital elements — especially carbon and nitrogen — between air, water, soil, sediment, and all living things. Understanding these cycles is important for a variety of reasons, but especially because they regulate Earth’s climate and support human civilization!
However, a key issue is that biogeochemical cycles have been heavily altered by various human activities. Climate change is an important part of this, but there are other types of change that are also important. Collectively we refer to this as ‘global change.’ Microbes can be very responsive to these changes, and their responses can alter biogeochemical cycles. This is cutting edge research that you will learn about.
8.1 Microbes and biogeochemistry. In this video lecture I’ll start to put together some of the microbial pieces of biogeochemical cycles. This is a little longer than some of the previous video lectures, but as always, pause, stop, rewind, and take notes!
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8.2 The carbon cycle. This NASA article on the carbon cycle provides an introduction to many different aspects of the carbon cycle. Be sure to read all the sections down to the references—the sections load as you scroll down.
You should pay attention to a couple of key points, some of which should be familiar to you from this course and others:
(1) Although carbon dioxide plays a key role in regulating Earth’s climate, most carbon on Earth is **not** found as carbon dioxide in the atmosphere. Understanding how those large pools of carbon (fossil fuels, soils, the ocean) are connected to the atmosphere is extremely important, as small changes in these pools can have a large effect on the atmosphere.
(2) Humans are effectively taking carbon from one large pool (fossil fuels) and moving it to the atmosphere. In effect, we are rapidly accelerating a slow geologic cycle.
(3) As large as the anthropogenic (human-generated) carbon flux is, it is dwarfed by natural fluxes, especially photosynthesis and respiration of carbon on land and in the ocean. Natural processes have absorbed about half of the carbon emitted to the atmosphere by humans, effectively saving us from some global warming. Exactly how this occurs, and whether it will continue, are topics of intense scientific scrutiny.
https://earthobservatory.nasa.gov/features/CarbonCycle
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8.3 Methane. Methane is a smaller aspect of the overall carbon cycle, but methane is a potent greenhouse that is much stronger than CO2 (although it also has a lower concentration and doesn’t last as long in the atmosphere). We spent a lot of time earlier learning about methanogenesis, which only occurs in the strict absence of oxygen (take a look at the redox ladder!). We also learned that there are microbes that oxidize methane, as it is a good source of energy (take a look at the redox ladder!). The methane cycle is complicated because of this internal methane cycling and because: (1) methane can also be produced abiotically; (2) there many different places where methane can be produced biologically; and (3) humans have altered some of these dramatically.
Let’s take a closer look at this figure of the methane cycle, which we have seen before. In all of these biogeochemical cycles, scientists try to compile budgets that represent different fluxes of a compound (shown by arrows). This is compiled by scientists as part of the Global Carbon Project. Natural sources are green and anthropogenic (human-caused) sources are orange. The thickness of the arrows, and the numbers above, show the size of the flux.
Let’s go left to right, starting with some ‘sinks’ for methane in the atmosphere. Carbon dioxide stays in the atmosphere for a while, and the main removal process from the atmosphere is actually photosynthesis. In contrast, methane is eventually destroyed in the atmosphere, primarily due to the action of hydroxyl radical. There is a ton of interesting atmospheric chemistry represented by the left three arrows. You should learn about it in other ESS courses!
Then we get into different production mechanisms (and one more sink) as we go left to right. Hydrates represent methane that is frozen in water in the deep ocean. This is interesting and worth a Google search. While a small source, there is concern about their stability.
Then freshwater is a significant natural source. This is because flooded sediments are anoxic and methane can be produced by methanogens. A lot of this methane is oxidized before it reaches the atmosphere (which we discussed in the land-sea/freshwater lectures).
The largest natural source, like we talked about, is wetlands. This includes a variety of soils that are flooded regularly (e.g., the Amazon) or more sporadically (e.g., vernal pools behind campus). As you know by now, water fills the pore space, oxygen is used up, methane can be produced by methanogens…
Moving left to right, we get to the final sink for methane, microbial oxidation in soils. While this is small compared to the atmospheric sink, it is significant and important if it changes in the future.
There are also natural geological sources of methane. Methane is produced (alongside oil) when organic matter is compressed and heated below the surface of the earth. Sometimes we capture this natural gas on its own (see the right side of the diagram), or alongside the oil, but some can escape naturally. There are various types of methane seeps etc. that make up this natural flux.
Moving left to right, we arrive at two large anthropogenic sources of methane. Because of the way we grow rice (in flooded fields), and we grow so much of it for food, it is a large source. Ruminant livestock are also a large source. This is due to methanogens living in their anoxic digestive tracts, and most of the methane is emitted in their burps. Again, because we grow so many more livestock than in the past, this is a significant anthropogenic source. Scientists are researching ways to reduce both of these fluxes.
Termites are then an interesting natural source. To be precise, this comes from methanogens living in termite guts. There are also microbes that produce hydrogen gas living in termite guts. Because termites and their gut microbes can digest wood and produce combustible gases, there is interest in how we might be able to replicate this process to generate energy!
Picture of termite mounds from the Global Carbon Project
Methane is also emitted during fires, which could be natural or have a human component. This isn’t microbes at work, just chemical reactions.
Finally we get to two large anthropogenic sources on the right side of the diagram. Lots of organic matter is buried in landfills, which can be converted to methane. An interesting example of this is that the city of Mountain View, CA, built a large amphitheater (Shoreline Amphitheater) on top of an old dump. They thought that they had sealed off and captured the methane, but enough was leaking out that occasionally it would catch on fire! There is now a lot of interest in capping landfills and collecting the methane coming out, as it is basically a free source of energy. It is also possible to specifically break down waste in way that will produce methane and other gases that can be burned.
Finally, the use of methane and oil as energy sources leads to lots of leakage to the atmosphere. Again, there is interest in trying to reduce this, as it represents lost energy and profit for the fossil fuel industry, while it is also a significant source of methane. Plugging these leaks would be a win-win.
Here are some additional articles on methane that you might be interested in:
https://www.sfgate.com/sf-culture/article/shoreline-amphitheatre-history-open-concerts-15594391.php
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8.4 The nitrogen cycle. Although the carbon cycle is incredibly important and has been altered by humans (with major consequences), the nitrogen cycle is connected to the carbon cycle and has been more heavily altered than the carbon cycle. Nitrogen is an important nutrient required by all organisms: life relies on proteins to catalyze reactions and build biomass; proteins are made of amino acids; amino acids contain an amine group; and that amine group contains nitrogen. The nitrogen paradox is that 78% of the atmosphere is nitrogen, but this is inaccessible to most organisms. Only specialized microbes and humans have figured out how to access atmospheric nitrogen and use it as a nutrient.
Humans have increased the rate of nitrogen cycling on Earth nearly three-fold, mostly through the production and use of synthetic fertilizers. This has increased crop production dramatically (part of the Green Revolution) and allows us to feed billions of people. However, we have an issue of nitrogen oversupply and overuse in some regions, and undersupply and underuse in other regions. The food that we grow doesn’t always make it to those that need it most. In addition, only about half the fertilizer that is applied to crops is taken up by the plants. Some of it is converted to gaseous forms that are important air pollutants (nitrogen oxides) and greenhouse gases (nitrous oxide). Some of it ‘runs off’ agricultural fields and can result in eutrophication and dead zones.
We’ve learned about some of the microbial processes involved in the nitrogen cycle, and this article connects them together:
Also review this article on nitrogen fixation if you did not read it a few weeks ago:
https://www.nature.com/scitable/knowledge/library/biological-nitrogen-fixation-23570419/
Finally, here is a recent article that discusses adding bioengineered microbes to agricultural fields. Do the benefits outweigh the risks?
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Beman Lab, University of California, Merced 