Microbiology For Dummies
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Not only are microorganisms extremely widespread, but within the microbial world there is also an impressive number of different metabolic pathways. You know this because of the compounds that they consume and produce, as well as from the study of microbial genes found in nature.

Recently, scientists have been able to sequence the full genomes of many microorganisms, giving them access to the sequences of all the genes present. This offers a glimpse into the metabolic potential of a microbe because knowing the genes present can suggest which enzymes the microbe can make and use for its metabolism.

Four broad categories of metabolic diversity include: the main energy-gathering strategy used, strategies for obtaining carbon, essential enzymes for growth, and products not essential for survival called secondary metabolites.

Getting energy

There are three sources of energy in nature:

  • Organic chemicals (those containing carbon–carbon bonds)

  • Inorganic chemicals (those without carbon–carbon bonds)

  • Light

Chemoorganotrophy is the type of metabolism where energy comes from organic chemicals, whereas chemolithotrophy is the type of metabolism where energy comes from inorganic chemicals. Phototrophy involves turning light energy into metabolic energy in a process called photosynthesis, and it comes in two main forms:

  • Oxygenic photosynthesis generates oxygen and is used by the cyanobacteria (a type of bacteria) and algae (a eukaryote), as well as all living plants.

  • Anoxygenic photosynthesis does not make oxygen and is used by the purple and green bacteria (types of bacteria that live in anaerobic aquatic environments).

Capturing carbon

All living cells need a lot of carbon, which is part of all proteins, nucleic acids, and cellular structures.

Organisms that use organic carbon are called heterotrophs; chemorganotrophs fall into this category. Organisms that use carbon dioxide (CO2) for their carbon needs are called autotrophs; most chemolithotrophs and phototrophs are also autotrophs, which makes them primary producers in nature because they make organic carbon out of inorganic CO2 that is then available for themselves, chemoorganotrophs, and eventually all higher life forms.

Some organisms can switch between heterotophy when organic carbon is available and autotrophy when food sources run out; these organisms are called mixotrophs.

Making enzymes

Few compounds in nature are not degraded by microorganisms. The variety of compounds produced by them is great and not completely known. Their metabolic processes are essential for environmental nutrient cycling, and they are the primary producers that support all other life on earth.

Microbes are specialists at degrading compounds, from the simplest to the most complex and everything in between. They’re the only ones able to degrade resistant plant material (fiber) made from cellulose (building blocks used by plants to make their tough cell walls) and lignin (building blocks used by plants for rigid structure, as in wood and straw).

The microbes in the rumen (part of a cow’s or related animal’s stomach) of herbivores and the guts of termites are responsible for digesting these tough plant fibers. Fungi and bacteria are the masters of producing special enzymes to degrade complex food sources (hydrolytic enzymes) including all forms of plant and animal tissues, some plastics, and even metals.

Secondary metabolism

Microbial products that are not produced as part of central metabolism and are not essential for everyday activities are called secondary products. Many of these products are bioactive compounds useful in interacting with other organisms. Antibiotics are an example of a secondary product used to interact with other microbes.

Some plant pathogens produce substances that mimic plant hormones so that they can manipulate plant growth. Other microbes make molecules that are useful in communicating with other microorganisms, insects, and plants.

Knowledge of the metabolism of microorganisms can be used in a variety of ways. One way is to try to isolate them in culture. This isn’t always easy — there are many gaps in our knowledge of the metabolic diversity of most microorganisms.

It’s relatively easy to re-create the temperature and oxygen conditions, but in order to select for the organism you want and select against all the other organisms, you have to know one specific condition that is needed just for your organism of choice.

Here are some other ways that the knowledge of microbial metabolism has been useful in the advancements of science:

  • Microbial enzymes are used in molecular biology research. Bacterial enzymes such as Taq DNA polymerase (used for reproducing sequences of DNA) and restriction enzymes (used to manipulate pieces of DNA in a cut-and-paste fashion) have become invaluable research tools.

  • Microbes are used to express animal proteins or enzymes such as insulin. When scientists discover that a disease can be cured or treated with a certain protein or enzyme, it becomes very useful and efficient for them to be able to mass-produce the molecule in microbes.

  • Microbial systems are used as part of microscopic machines in synthetic biology. To conduct further research, scientists make use of what we know to push the envelope of engineering and genetics. Scientists use microbial processes to their fullest potential to create new things within organisms.

  • Industrial processes have taken advantage of the diversity of microbes in the food, pulp and paper, mining, and pharmaceutical industries (to name but a few). Because some microorganisms are tolerant of extreme conditions, the enzymes they produce are useful in industrial settings where conditions can be harsh.

Because scientists don’t know all the metabolic diversity in the microbial world, they haven’t been able to isolate in culture a vast number of environmental microbes. This has resulted in huge gaps in knowledge about all the microbial groups that exist.

The term microbial dark matter has been coined to describe the vast number of microbial lineages for which scientists know very little (and in most cases, almost nothing). Like the dark matter of the universe that makes up the majority of matter, microbial dark matter is enormous and likely outweighs the known biodiversity of the earth by several orders of magnitude.

About This Article

This article is from the book:

About the book authors:

Jennifer C. Stearns, PhD, is an assistant professor in the department of medicine at McMaster University. She studies how we get our gut microbiome in early life and how it can keep us healthy over time. Michael G. Surette, PhD, is a professor in the department of medicine at McMaster University, where he pushes the boundaries of microbial research.

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