Microbial Metabolism – The Weird and Wonderful Ways Microbes Get Energy.

A medical illustration of vancomycin–resistant, Enterococci sp. bacteria. Original image sourced from US Government department: Public Health Image Library, Centers for Disease Control and Prevention. Under US law this image is copyright free, please credit the government department whenever you can”.

I have an interest in the microbial world both through education and also my work, with that in mind I am often passionate about sharing some of the interesting and incredible ways that microbes can actually survive in the environment. In other posts, I have talked about some of the weird places microbes can survive, but in this post, I wanted to talk more generally about what microbes need to survive, and how they do it.

As with all of my posts, this is a combination of rambling, my thoughts, and a summarised set of information. It is designed as a very very basic overview and you can from there find other resources which outline these concepts further.

Before I get started, it is worth understanding what we mean by microbial metabolism. This refers to the way that a microbe can obtain the energy and also the nutrients it needs to live and reproduce. Microbes have evolved to have many different strategies for obtaining energy and nutrients and how they obtain this can be used to differentiate between microbes. It can also provide some information on the typical environmental/ecological niche in which the microbe falls.

How can we group based on metabolism?

We often group microorganisms based on their metabolism, and how they obtain energy and nutrients. Generally speaking, we are trying to understand how microbes obtain carbon for their cell mass, how the organism obtains reducing equivalents for energy conservation or biosynthetic reactions, and how the organism obtains energy for living and growing. We can then use this information to start to group based on metabolism.

When we talk about how carbon is obtained, an organism can be either:

  • Autotrophic – obtaining carbon from carbon dioxide (CO2).
  • Heterotrophic – obtaining carbon from organic compounds.
  • Mixotrophic – obtaining carbon from both organic compounds and also carbon dioxide.

When we talk about how an organism obtains reducing equivalents (which means how it obtains hydrogen atoms or electrons), organisms can be either:

  • Lithotrophic – obtaining reducing equivalents from inorganic compounds.
  • Organotrophic – obtaining reducing equivalents from organic compounds.

Finally, when we talk about how an organism obtains energy for both living and growing, it can be either:

  • Phototrophic – energy is obtained from light.
  • Chemotrophic – energy is obtained from external chemical compounds.

In terms of naming, it is usually (1) where they get their energy from, (2) where they get their reducing equivalents from, then (3) where they get their carbon from.

Organisms can be a mixture of these, for example, Chemo-Organo-Heterotrophs (dashes added just to show more clearly), where carbon is obtained from organic compounds, reducing equivalents are obtained from organic compounds, and energy is obtained from chemical compounds. Alternatively, Chemo-Litho-Autotrophs obtain carbon by fixing carbon dioxide, and energy from the oxidation of inorganic compounds.

It should be noted that microbes can be any variation of these, but often you find that there is a dominant group, for example when we look at chemolithotrophic microbes, most are autotrophic.


Microorganisms in this group use organic compounds for both energy sources as well as for carbon sources. To achieve this microbes live off nutrients that they either scavenge from living hosts (as either a parasite, or through potential symbiosis), through predation, or that they obtain in dead organic matter.

In the context of microorganisms, an example of a heterotrophic organism is the Amoebae which consume other microorganisms. Microorganisms that feed on nonliving organic matter are called a saprotroph or saprophytes with an example of this being many species of fungi including the species that causes wood rot Serpula lacrymans.

Whilst I don't want to go into the chemistry of metabolism, it is worth noting that the metabolic process requires a final electron acceptor (terminal electron acceptor), for many species oxygen is this terminal acceptor which means that the microbe requires oxygen to function, however, in some cases microbes are not able to tolerate the presence of oxygen and instead rely on a different terminal electron acceptor (like carbon).

Those microorganisms that use organic carbon instead of oxygen as a terminal electron acceptor are undergoing a process known as fermentation. Microbes that rely on oxygen are called Aerobic, those that cannot survive in the presence of oxygen are called anaerobic. In some species, the microbe has the ability to undergo aerobic respiration in the presence of oxygen, or anaerobic respiration/fermentation in the absence of oxygen (facultative anaerobe).

An example of an anaerobe is the bacteria responsible for botulism (Clostridium botulinum). An example of an aerobe is Pseudomonas aeruginosa. Finally, an example of a facultative anaerobe is Escherichia coli.

There are many more variations (for example aerotolerant anaerobes, and microaerophiles) that I have not covered with respect to their metabolism so if you are interested in this is worth having a look at some of those. In recapping through, heterotrophic microbes get their energy and carbon sources from organic materials (either dead or alive) but there are some differences in the metabolic processes which is around if oxygen is required or not.


Chemolithotrophs are microbes where energy is obtained from the oxidation of inorganic compounds. Whilst most chemolithotrophs are autotrophic (they get carbon from fixing carbon dioxide), some obtain their carbon from organic compounds. Chemolithotrophs can belong in the Bacteria and Archaea domains.

An example of a chemolitho(auto)troph is Thiobacillus which is an obligate autotroph (which means it gets energy from external compounds, reducing equivalents from inorganic compounds, and carbon from carbon dioxide), whereas an example of a ChemoLitho(hetero)troph is Desulfovibrio.

This is one of my favorite types of microbial metabolism as it is unusual compared to that of the heterotrophic microbes. There are lots of different types of chemolithotrophs that get their energy from different inorganic sources, these can include:

  • Iron oxidizing bacteria
  • Metal Reducing Bacteria
    • Iron (Fe(III))
    • Manganese (Mn(IV))
  • methanogens – metabolize methane for carbon and obtain energy from oxygen, nitrate, sulphate or other oxidized compounds.
  • Nitrifying Bacteria
    • Ammonia oxidizing bacteria (AOB)
    • Nitrite oxidizing bacteria (NOB)
  • Purple Sulfur bacteria
  • Hydrogen oxidizing bacteria
  • Sulfate-reducing microorganisms
  • anammox bacteria (anaerobic ammonium oxidisation)


Phototrophs are organisms that use light (photons) to generate energy and produce organic compounds. They can either be photoautotrophs where they obtain energy from light, and obtain carbon by fixing carbon dioxide, or they can be photoheterotrophs where they obtain energy from light, but they get carbon from organic compounds.

Most photoautotrophs take carbon dioxide and use chlorophyll and light to generate energy and to generate organic compounds. Plants are a larger scale example of a phototroph, but in the microbial world algae and even cyanobacteria are examples of photoautotrophs.

It is worth noting that there are also photolithoautotrophs that use light for energy, an inorganic compound as an electron donor, and carbon dioxide as a carbon source.

So what are the weird ways microbes get energy and nutrients?

Earlier in this post, I have highlighted the types of metabolism that take place which looks at how energy is obtained, how reducing equivalents are sourced, and from where carbon is acquired. Now it is worth putting this together to show some of the typical places microbes can get energy and some of the more unusual places.

The most typical of all life is a chemoorganoheterotroph in this case the microbe is getting most of what it needs from organic material (be it live or dead), then there are the photoautotrophs such as algae which get their energy, and larger examples of these are plants.

In my mind, the weirdest though are the chemolithotrophs (an interesting fact: the phrase means rock eater!). Chemolithotrophs have developed the ability to break down inorganic compounds which in the natural environment is important for many symbiotic relationships, nutrient cycling, and even the broader food chain.

These organisms are important in the natural environment (i.e., breaking down inorganic compounds) but because they can live inside pipes and other materials that contain inorganic compounds they can end up causing corrosion and premature breakdown or failure of the materials.

In another post, I discuss the weird places and environments microbes can live in, with many of these being chemolithotrophs. An example of this is the acid-loving bacteria Acidithiobacillus ferrooxidans which can live in mines and can use iron (and carbon dioxide) to drive their metabolism.

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