Metabolism

An organism’s metabolism — the sum of all the chemical reactions going on inside it — can be precisely defined by its energy source, its electron donor source, and its carbon source.

The Macro World

People who study plants, animals, and/or their metabolisms don’t typically focus on this level of detail. It’s simply taken as read that in the macro world plants photosynthesise to make their own food, while animals must eat to obtain theirs. It matters not whether the spark of life comes from photons or chemical bonds, or whether electrons originate from inorganic or organic compounds — it is what it is — and ‘metabolism’ is taken to be all the important stuff which happens after that.

The Micro World

All this changes in the microbial world however, where these distinctions do have great significance and importance. This is especially so in soil and water environments, where nutrient availability and recycling is possible only because of some truly unique microbial metabolisms.

Classifications of Metabolic Modes

All metabolic types can be classified by energy source, electron donor source, carbon source, and all combinations of these. 

By Energy Source

Phototroph: energy source is photons (phototrophs are not automatically photosynthesisers, though all photosynthesisers are phototrophs)
Chemotroph: energy source is chemical bonds

By Electron Donor Source

Lithotroph: electrons from inorganic compounds
Organotroph: electrons from organic compounds

By Carbon Source

Autotroph: carbon from inorganic compounds
Heterotroph: carbon from organic compounds

By Combining Energy and Electron Donor Sources

Photolithotroph: energy from photons, electrons from inorganic compounds
Photoorganotroph: energy from photons, electrons from organic compounds

Chemolithotroph: energy from chemical bonds, electrons from inorganic compounds
Chemoorganotroph: energy from chemical bonds, electrons from organic compounds

By Combining Energy and Carbon Sources

Photoautotroph: energy from photons, carbon from inorganic compounds (these are the photosynthesisers)
Photoheterotroph: energy from photons, carbon from organic compounds (these are not photosynthesisers)

Chemoautotroph: energy from chemical bonds, carbon from inorganic compounds
Chemoheterotroph: energy from chemical bonds, carbon from organic compounds

By Combining Electron Donor and Carbon Sources

Lithoautotroph: electrons from inorganic compounds, carbon from inorganic compounds
Lithoheterotroph: electrons from inorganic compounds, carbon from organic compounds

Organoautotroph: electrons from organic compounds, carbon from inorganic compounds
Organoheterotroph: electrons from organic compounds, carbon from organic compounds

By Combining Energy, Electron Donor, and Carbon Sources

Photolithoautotroph: energy from photons, electrons from inorganic compounds, carbon from inorganic compounds
Photolithoheterotroph: energy from photons, electrons from inorganic compounds, carbon from organic compounds

Photoorganoautotroph: energy from photons, electrons from organic compounds, carbon from inorganic compounds
Photoorganoheterotroph: energy from photons, electrons from organic compounds, carbon from organic compounds

Chemolithoautotroph: energy from chemical bonds, electrons from inorganic compounds, carbon from inorganic compounds
Chemolithoheterotroph: energy from chemical bonds, electrons from inorganic compounds, carbon from organic compounds

Chemoorganoautotroph: energy from chemical bonds, electrons from organic compounds, carbon from inorganic compounds
Chemoorganoheterotroph: energy from chemical bonds, electrons from organic compounds, carbon from organic compounds

Examples

The Macro World

If classified by energy source only, plants are phototrophs (energy from photons) and animals are chemotrophs (energy from chemical bonds in oxygen).

If classified by electron donor source only, plants are lithotrophs [electrons from (inorganic) water] and animals are organotrophs (electrons from organic compounds — carbohydrates, proteins, fats).

If classified by carbon source only, plants are autotrophs [carbon from (inorganic) carbon dioxide (CO₂)] and animals are heterotrophs (carbon from organic compounds — carbohydrates, proteins, fats).

These terms can be combined: plants are photoautotrophs, photolithotrophs and lithoautotrophs, and animals are chemoheterotrophs, chemoorganotrophs and organoheterotrophs.

Combining these further specifies the complete metabolism of any organism by its energy source, electron source and carbon source. Here, plants are photolithoautotrophs and animals are the exact opposite chemoorganoheterotrophs. (Plants do switch to chemoorganoheterotrophy in the absence of light so as to process the carbohydrate food they made during sunlight — this makes them mixotrophs as well: organisms able to change metabolic modes.)

These are the only two metabolisms in the macro world of plants and animals, which may be why they’re never mentioned as such. ‘Plant’ and ‘animal’ is just as informative, without needing pretentious and unnecessary words like ‘photolithoautotroph’ and ‘chemoorganoheterotroph’. In fact, these words actually arose from microbial studies in the first place, and are practically unknown outside of it.

Having said this, there is still some value in knowing how to interpret these words, as they actually do clarify plant and animal metabolisms more clearly than ‘plant’ or ‘animal’ can. For example, most people think that plants are like us, but the opposite, in that they ‘breathe in’ carbon dioxide and exhale oxygen, while we do the reverse. It’s completely understandable to think this, and fits the idea of a perfectly balanced world with each side providing ‘breathable’ air for the other.

Yet this isn’t quite what is going on, and it is only from the fancy words that the secrets are revealed!

The first clue is in the photo- versus chemo- part. Chemo- here refers to the oxygen we breathe — this is our chemical energy source which initiates all further biochemical processes. The chemical bonds of oxygen gas molecules are broken inside us to release this energy, and we must continuously breathe so as to replace this spent oxygen and energy source. All biochemical reactions inside us will stop completely if oxygen is not constantly brought in to drive them.

If plants ‘breathed in’ carbon dioxide, or oxygen, or nitrogen, or any other chemical, then they too would be chemotrophs. But their energy source is photons, making them phototrophs.

The second clue is in -auto- versus -hetero-. This reveals the carbon source. -Auto here refers to the inorganic carbon dioxide plants take in, while -hetero refers to the organic carbon we take in as carbohydrates, fats and proteins. Carbon dioxide isn’t ‘breathed in’ by plants; it is, loosely speaking, ‘eaten’ and converted into carbohydrates! Carbon dioxide is used by the plant as a carbon source, whereas heterotrophs use oxygen as an energy source. Heterotrophs exhale carbon dioxide as a toxic waste product of cellular respiration, while plants expel oxygen as a non-toxic waste product of photosynthesis.

Plants are photoautotrophs, the photosynthesisers, making carbohydrates from sunlight and carbon dioxide. It’s worth mentioning though, that in darkness plants become animalistic and switch to chemoheterotrophy, as it is only in this state that they are able to use the carbohydrates they made as food. Roots are always in chemoheterotrophy by the way, as they are incapable of photosynthesis. They also take in oxygen just as we do, and expel carbon dioxide. Carbon dioxide is also released as a waste product by the rest of the plant when in chemoheterotrophy.

The Micro World

Everything changes in the microbial world, in which there are eight possible combinations of energy source, electron source and carbon source (as listed above). These lengthy words have far more importance and relevance here, as they explain the chemical reactions of these single-celled organisms and their role in nature more clearly.

Of the two metabolic modes found only in the macro world, photosynthesising bacteria are the plant-equivalent photolithoautotrophs, while all fungi, some bacteria, and some archaea are the animal-equivalent chemoorganoheterotrophs.

The remaining six metabolic combinations are all unique to the microbial world. Some are rarer than others, but all can be found in at least one species. Many species, like plants, are also mixotrophs.

Significance

Ask someone to think about ‘carbon’, and they may picture coal, charcoal, fossil fuels, or maybe even wood and ash — all of which were once life. Asked to think about hydrogen, oxygen, nitrogen, sulfur, iron, copper, or any other element, and first thoughts will probably be of the air, hot springs, rocks or in the ground — the never-living world in other words.

This simple exercise reflects our instinctive understanding of the origins of ’stuff’, even if we can’t articulate this: that life is carbon-containing ‘organic’ material, while non-life is ‘mineral’, or inorganic non-carbon-containing material.

All organic molecules contain carbon, but they also contain inorganic hydrogen and oxygen. Some additionally contain elements such as nitrogen, sulfur, magnesium, iron and phosphorus, just to name a few. Still other elements such as chlorine and copper aren’t part of organic molecules but still have important biochemical roles as free ions and catalysts.

Life is organic, but impossible without the inorganic.

Yet while we breathe in inorganic air for the oxygen, we can’t make use of a single atom of the 78% nitrogen in that same air. Nor can we make use of the carbon in the 0.04% inorganic carbon dioxide also breathed in. Or chew on dirt and rocks for a quick iron or copper fix. How then, do these elements become bioavailable?

Enter those six metabolisms found only in microbes! We cannot directly access the inorganic ‘mineral’ world, but many microbes can. We, like all other life on Earth, are wholly reliant on microbial metabolisms making non-life ‘minerals’ available to living organic matter at all. These uniquely-microbial metabolisms made possible life from non-life, and these same metabolisms ensure that all essential elements continue to be recycled from life, to non-life, and back.

Importance in Nutrient Recycling

The Macro World

Plants use photons and water to convert, or ‘fix’, unavailable inorganic carbon dioxide into available organic carbon in the form of carbohydrates.

This crucial step literally makes out of air bioavailable carbon that can enter the food chain and make macro life possible. Carbon from carbon dioxide becomes carbon available to feed both the plant and any herbivores which eat that plant, and ultimately the carnivores which feed on the herbivores and other carnivores. This consumption of carbon-rich plant and animal tissue is also the only way by which essential inorganic elements (magnesium, iron, calcium, copper, and others) can enter the food chain.

Plants can only make inorganic carbon available to other lifeforms however. They cannot convert inorganic nitrogen, calcium, sulfur, phosphorus, potassium, iron, or any other essential element into a life-friendly form. If not recycled by other means, these elements would eventually accumulate in greater and greater concentrations of inaccessibility in dead animals at the top of the food chain. All life would eventually become extinct without a means to recycle its components.

The Micro World

Only microbes are capable of recycling all essential elements, meaning all life on Earth is wholly dependent on them and their unique metabolisms to do so.

For example, nitrogen is essential for the formation of amino acids, DNA and RNA, but is completely inaccessible to most life in its gaseous state, just as the carbon in carbon dioxide is unavailable to most life in its gaseous state. Microbes are the only organisms (collectively) capable of pulling nitrogen out of the air and enabling its flow through ecosystems by converting it firstly into ammonia, then ammonium, nitrites, nitrates, and finally back to nitrogen gas for return to the atmosphere.

This is the nitrogen cycle, and many microbial species covering most, if not all eight metabolic modes, are essential for this cycle to go to completion. The autotrophic species involved have additional importance as they are fixing carbon dioxide and inputting organic carbon as well as nitrogen into their ecosystems!

This is just the nitrogen cycle — there is a sulfur cycle, phosphorus cycle, calcium cycle, iron cycle, and many more collectively called biogeochemical cycles. There are mercury and hydrogen cycles too! Microbes feature in every single one as each element is cycled from the atmosphere, lithosphere and hydrosphere, through the microbial biosphere, and back again.

The lithotrophs have very important roles in these cycles — they are the ‘rock eaters’ after all! They use iron, or sulfur, or phosphate, or nitrite, or any number of ‘minerals’ as we use carbohydrates, proteins or fats.

With the exception of plants, which are photolithoautotrophs, every other lithotrophic species is microbial. Not a single chemolithotroph exists in the macro world. Many lithotrophs are also mixotrophs, able to switch from phototrophy to chemotrophy, or autotrophy to heterotrophy. Some can even switch between lithotrophy and organotrophy! Some can be any mix of any of these, and able to take full advantage of changes in their environments.

In Conclusion

A complete definition of metabolism includes an organism’s energy source, electron donor source, and carbon source, for a total of eight possible combinations.

Only two of these eight exist in the macro world: plants are photolithoautotrophs and animals are the exact opposite chemoorganoheterotrophs. These terms are of little importance and never mentioned in scientific fields at this level.

It is only the microbial world which has all eight metabolic combinations, and where these terms become very meaningful and relevant. Knowing that any particular microbe is autotrophic, chemotrophic, and/or lithotrophic or mixotrophic helps to understand the variety of ways microbes are able to obtain energy and feed themselves — especially if these mechanisms are completely alien to those of plants and animals.

It is because some metabolisms are so different to those of plants and animals that microbes can convert the essential elements of non-living matter into bioavailable forms at all. And it is the presence of all metabolic types within an environment which ensures these elements continue to flow through ecosystems until they are returned to non-living forms for the cycle to begin anew.

These cycles are called biogeochemical cycles, and are the way by which the four major spheres of Earth interact to form a fifth: the pedosphere, or soil. These interactions which create the pedosphere are collectively known as pedogenesis, or soil formation.

Awareness of the various microbial metabolisms helps to understand how nutrients are made plant-available through pedogenesis and nutrient-cycling. This in turn helps to understand the interactions between soil, microbes, and plants, and that in turn helps to understand the whole concept of ‘From Soil to Fruit’. All of this will be covered in more detail in other chapters.