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 and Earth History
This week we will focus on what exactly microbes are and their role in Earth history. It turns out that they have completely altered the chemical composition of the planet. They also represent the longest chapter in the history of life, having inhabited the planet for billions of years (and counting).
Each week we will have a mix of content, usually between 5 and 9 of the following: videos to watch, pages to read, interactives to explore, etc. These will be assembled together into a ‘series,’ and you can either binge the whole thing or take it a step at a time. This week you have seven things to do:
2.1 What are microbes? This video lecture provides an introduction to microbes – i.e., what are we talking about in this course?!?
As with all these video lectures, pause, rewind, and take notes as needed. Pay special attention to slides with bullet points, and to any figures displaying information.
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2.2 Viruses. This is an interactive from the Howard Hughes Medical Institute (HHMI) that provides an introduction to a few different types of viruses. As you learned in the previous lecture, viruses are microbes, but are obviously not free-living organisms—they infect their host organisms in order to reproduce. As is painfully clear right now, viral hosts can obviously include humans, as well as many other large organisms, and viruses can also infect other microbes.
This interactive shows a few of these different viruses and provides different information on them.
Be sure to:
-Read the ‘About’ and ‘Key Concepts’ at the bottom of the page.
-Then click through and explore the different viruses.
https://media.hhmi.org/biointeractive/click/virus-explorer/index.html
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2.3 Photosynthesis. This video lecture provides an introduction to photosynthesis, which is critically important in sustaining life on our planet. When we look at the history of life on Earth—which is mostly microbial—photosynthesis is central:
-Photosynthesis produces material/food/energy that is used by nearly all living things
-The production of oxygen provides a key marker in time, and changed the chemistry of the planet
As with all these video lectures, pause, rewind, and take notes. Pay special attention to slides with bullet points, and to any figures displaying information.
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2.4 Photosynthesis in space and time. This animation from NASA includes much useful information on photosynthesis and clearly illustrates variations that we see in space and time. Please watch the whole video with sound on to hear from the NASA scientists:
https://svs.gsfc.nasa.gov/vis/a010000/a012900/a012945/LivingPlanetfromSpaceFINE_high.mp4
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2.5 How photosynthesis works… and the implications. We just learned about the importance of photosynthesis and wrote an equation that you have probably seen many times:
6CO2 + 6H2O –light–> C6H12O6 + 6O2
Photosynthesis uses a series of reactions powered by light energy to convert carbon dioxide (CO2) and water (H2O) into organic material of some kind (e.g., glucose; C6H12O6) and produce oxygen (O2).
But it turns out that this is not the only equation for photosynthesis, or the only type of photosynthesis! This is also an equation for photosynthesis:
6CO2 + 12H2S –light–> C6H12O6 + 12S + 6H2O
The first process is far more common on the present Earth and is oxygenic photosynthesis. The second equation represents anoxygenic photosynthesis. We can still find habitats where this occurs (they’re cool; see info below), but notice the differences: anoxygenic photosynthesis does not produce oxygen (O2)—hence the name—and it does not utilize water (H2O). Instead, anoxygenic photosynthesis uses hydrogen sulfide (H2S)—which is a gas that has a notorious ‘rotten egg’ smell that you might smell in a coastal area or in a feedlot. There is also another type of anoxygenic photosynthesis, and both are conducted exclusively by microorganisms.
Photosynthesis, more broadly defined, uses light energy to oxidize (pull electrons from) one compound and reduce (funnel electrons to) carbon dioxide (CO2) to produce organic material. We will spend much more time on redox reactions and how microbes use them.
When scientists started to examine the different types of photosynthesis in more detail, multiple major findings revealed a great deal about life on our planet:
1) First, the oxygen (O2) produced during oxygenic photosynthesis comes from water. The oxygen (O2) that they produce does not come directly from carbon dioxide (CO2)—this is a common misconception. Water is actually broken apart during the ‘light reactions.’ This is amazing when you think about it: plants and phytoplankton really, truly need water because they actually destroy it! They produce oxygen (O2) as a waste product, and use electrons from water in subsequent reactions.
This is what I meant earlier about water, photosynthesis, and oxygen all being connected: water is converted by oxygenic photosynthesis to the oxygen present in the atmosphere. How much hydrogen sulfide (H2S) is on Earth? Not a lot. How much water is on Earth??? A lot! Using water is a huge advantage over other compounds.
2) How does oxygenic photosynthesis do this? Well it turns out that two earlier forms of anoxygenic photosynthesis were fused together. We see a very clear relationship between two distinct types of reaction centers (RC) present in two groups of anoxygenic photosynthetic organisms, and two photosystems (PS) that are combined together in oxygenic photosynthetic organisms. Here is a figure of this from a review article by Fisher et al. (2016):
This is a complicated diagram, but you will understand most of it by the end of the class! The most important point is that the ‘machinery’ of oxygenic photosynthesis is on the left, and the two forms of anoxygenic photosynthesis on the right. Different enzymes are listed at bottom left. Note the similarities!
The organisms involved are also listed within the color shaded boxes. The cyanobacteria were the first oxygenic photosynthetic organisms. They are still hugely important in the ocean today. They were responsible for most of the oxygenation of Earth’s atmosphere. And they are microbes in the domain bacteria. We know that other oxygenic photosynthetic organisms evolved from the cyanobacteria.
3) This combination of geochemistry, molecular biology, paleontology, etc. allows us to go back in time. Multiple clear signals show us that oxygen built up in the atmosphere around 2.5 billion years ago—but this build-up would have taken some time. From various fossils, we also know that oxygenic photosynthesis—especially those cyanobacteria—probably evolved ~2.8 billion years ago.
We now know that they evolved from earlier forms of anoxygenic photosynthesis, so we can trace those lineages back in time. They in turn probably evolved from non-photosynthetic organisms. This places the evolution of life early in Earth history, possibly 3.5-3.8 billion years ago (Earth is 4.6 billion years old). In the next interactive, you will see all of this on a timeline, and see the isotopic evidence for when life was first active on Earth.
Finally, while oxygenic photosynthesis is dominant on Earth, anoxygenic photosynthesis still occurs, and these ancient organisms are still present—which is cool to think about. We see lots of them in one of our field sites, Jellyfish Lake, Palau. Check out these videos of a camera being lowered down through Jellyfish Lake, and learn more through the link. The bright pink layer is made up of anoxygenic photosynthetic bacteria.
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2.6 Deep history of life on Earth. This is another HHMI interactive that allows you to explore the history of life on Earth along a timeline. Be sure to:
-Read the Introduction at top right
-Note the Great Oxidation Event around 2.5 billion years ago
-Go backwards on the timeline and watch the linked videos on (1) biomarkers, and (2) especially chemical evidence for life
https://media.hhmi.org/biointeractive/click/deeptime/
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2.7 Early Life. Please read this article from Quanta magazine—and watch the video at the end—about early life:
https://www.quantamagazine.org/a-new-step-in-re-creating-first-life-on-earth-20160825/
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Beman Lab, University of California, Merced 