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.
Mix, Match, and Redox
This week we will be talking about oxidation-reduction (redox) chemistry. I’m here to tell you that it is super interesting. I know, I know, you think that you will disagree as soon as I mention ‘delta G.’ But redox chemistry ends up explaining fascinating patterns that we see in microbial activity in the environment.
3.1 Redox Chemistry. Redox chemistry helps explain how nutrients are cycled in different environments; it explains when and where the important greenhouse gas methane is produced; and it explains the age-old question “why does stuff stink?” I know this sounds a little ridiculous, but please stick with me and you will see how this sets up our understanding of microbiology, ecology, and biogeochemistry in all habitats.
You probably remember calculating the Gibbs free energy in chemistry and a figure like this:
If two reactants can produce two products and yield energy, the reaction is thermodynamically favorable. However, there is also an activation energy associated with the reaction (remember that this is the initial ‘hill’ shown in the figure). You probably remember from biology and/or chem that enzymes act as catalysts, reducing the activation energy for a reaction. What is interesting about microbes are the following three things:
1) They have evolved enzymes and electron transport chains that allow them to make use of almost any energetically favorable reaction—even involving compounds that are toxic to us. Most large organisms are pretty boring in what we eat (organic matter of some form) and breathe (oxygen gas). But microbes can ‘eat’ and ‘breathe’ almost anything. (Note that they don’t actually ‘eat’ or ‘breathe,’ they have to transport compounds into a single cell.) Scientists are actually still discovering new forms of metabolism for microbes!
2) Some microbes have multiple capabilities. As we know all too well, if we don’t get enough oxygen we will die. But some microbes are able to adjust to radically changed conditions—even the absence of oxygen, known as anoxia or anaerobic conditions—by activating different pathways.
3) Even for microbes that use the same compounds, different enzyme systems and pathways allow them to occupy different niches. Some may be specialists, some may be generalists. Some may have high affinities for different compounds that allow them to occupy challenging environments, while others may act as microbial ‘weeds’ that do best under disturbed conditions.
We will discuss all of this as we progress through the course, and redox chemistry sets this all up. So I wanted to provide a brief review of some of the basics of redox chemistry, and then introduce the concept of the ‘redox ladder,’ which is extremely useful for explaining patterns in the environment—such as during irrigation/flooding of soil, or with depth in a lake or the ocean.
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3.2 Redox Intro. This video lecture provides a quick introduction to redox chemistry to remind you how it works. We will then dive into the details of why this is important in the environment.
The key concept that we will use is the ‘redox ladder,’ as it helps us explain interesting patterns in the environment. We aren’t focused on calculating redox states for individual compounds, or delta Gs from individual reactions, but how it all fits together!
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3.3 More Redox (if needed). If you aren’t as familiar with redox chemistry, and or can’t remember much of it, here are some useful resources to review. The first is a Crash Course Science video, followed by two lectures from an online chemistry course at UC Irvine (just watch the first 10-15 minutes of the second lecture unless you want more time/practice with balancing chemical equations).
Also note that in our class, we are focused on the elements C, N, and S, and how they bond with O and H. So this why we really only need to remember a few of the redox rules.
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3.4 Redox Ladder Figure. As you’ve learned, the redox ladder is a useful way of organizing different processes that can occur in the environment. We will go into this in greater detail here and in the following lecture. The basic idea is that microorganisms can combine various oxidants and reductants to generate energy. It is more complicated than pure chemistry due to the enzymes and electron transport chains that microorganisms possess, but, in general, there is a consistent progression in time or space based on the energy available from a particular pair oxidant/reductant pair. These are shown on the redox ladder on the right side of this diagram from our old textbook, Environmental Microbiology by Madsen.
Before we look at the ladder, what I really like about this diagram is that it includes other aspects of ecology that you may have learned in the past, as well as the importance of photosynthesis that we covered in Week 2. On the left side of the figure, you can see that energy that comes in from the Sun is actually used by oxygenic photosynthesis to break apart water (do I need to say this again ;). The oxygen (O2) that is produced is shown by the upper arrows. The lower arrows show classic concepts in ecology: the organic material that is produced by primary production fuels the trophic pyramid (e.g., producer -> herbivore -> predator -> apex predator). Some material also becomes detritus (which can be recycled), and some goes directly to ‘prokaryotes.’ You may remember that this term refers to non-eukaryotes, i.e. bacteria and archaea.
Now to the ladder on the right side. The far right side shows a numerical scale with the redox potential (pE) and the energy available in kJ. The greater the separation on the ladder, the greater the energy available. To the left of the scale, a series of compounds are written on the left and right side of a vertical line. You probably recognize many of these. On the left side are potential oxidants, running down from O2 at the top. On the right side are reductants, running up from organic material (CH2O) on the bottom. These can be connected by the flow of electrons from reductant to oxidant (shown as an arrow).
The greater the separation, the greater the energy yield. So what we see is that the combination of O2 as an oxidant and with organic matter (CH2O) as a reductant generates a lot of energy! They are widely separated on the ladder. This chemical reaction is respiration, and how you and I generate energy in our cells. (Note that we also use this reaction to generate energy when burning fossil fuels, and this also occurs in fires—in all cases, organic matter is being oxidized by oxygen. ) I mentioned this as a very important aspect of oxygenic photosynthesis: it produced a lot of energetic oxidant (O2 ) and reductant (CH2O). Go back if you don’t understand this, as it is important.
As we will see in the following lecture, many organisms then use either oxygen as an oxidant or organic matter as a reductant. Many combine the two together, but others can use other oxidants or other reductants. This is what we will discuss in the lecture, and is important because many of the compounds that are produced and consumed are very important.
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3.5 Up and Down the Redox Ladder. This video lecture goes through some of the key steps on the redox ladder. As you will see, the relationships between where different compounds fall on the redox ladder ends up explaining some patterns that we see in the environment. I mean, that’s the whole point of this 🙂
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3.6 Winogradsky Column. This HHMI interactive describes a ‘Winogradsky column,’ which is an interesting and easy illustration of redox in the environment.
First read the ‘Background’ tab. This gives an overview of a Winogradsky column (including the name) and the science behind it. Definitely study Table 1. We will spend more time on this as we go through the course. We will be continually organizing microbes by their energy source and carbon source (and also electron donor). Over time, this jargon will make more sense. Also check out the redox animation.
https://media.hhmi.org/biointeractive/click/winogradsky/
Then look at the ‘Interactive Column’ diagram. Slide the box with arrows down through the column to see the different microbial groups and processes that are found at different depths in the column. There is a lot of information here! But be sure to check out how the metabolic niches change with depth, and how different bacteria inhabit these niches.
We have already seen a few of these before: oxygenic photosynthesis up top, heterotrophic respiration below it; below iron reduction, there are three groups of sulfur-cycling bacteria—these are the anoxygenic photosynthetic bacteria that we learned about in week 2. (The purple sulfur bacteria are those organisms that gave that pink/purple tint to the profiles through Jellyfish Lake in Palau.) They are using hydrogen sulfide (H2S)—that rotten-egg smelling gas—produced by other organisms (sulfate-reducing bacteria) as a source of electrons during photosynthesis. This is an example of how multiple interacting groups depend on each other for energy, and this concept is important when we think about how elements are cycled in the environment.
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3.7 Winogradsky Column Time-lapse. This is a time lapse of a Winogradsky panel (which is wider than a column) that is actually from a scientific paper. The authors were examining the microbial ecology in more detail.
The main thing to observe is how conditions visually change over time, and this is due to the activity of microbes! In particular, the green and pink colors are the pigments present in different photosynthetic organisms. The black color is due to hydrogen sulfide being produced, which can react with minerals and lead to the color change.
This gives you an idea of how redox conditions can change and fluctuate—even in a controlled experiment.
Beman Lab, University of California, Merced 