Anaerobic microbiology: meet the organisms that survive and thrive without oxygen

Most of the life that we see around us, like plants, animals, humans, depends on oxygen for survival and growth. But while macroorganisms are aerobic creatures, there is a whole world of microorganisms called anaerobes that don't need oxygen to survive. And for some of them, oxygen can even be deadly.

Anaerobic environments are more common than you might think. They include sediments, soil micropores, biofilms, and even our very own digestive system. Humans also harness anaerobic organisms to produce fermented foods and break down wastes. Let's explore the origins of anaerobic metabolism, some environments that are dominated by anaerobes, and the ways in which human life depends on the activity of anaerobic microorganisms.

The oxygen-free world: origins of anaerobic metabolism

The current concentration of oxygen in the atmosphere is ideal for complex organisms like animals and plants. But for the first half our planet's life, Earth's atmosphere was almost completely free of oxygen.

Then, somewhere between 3.5 and 2.5 billion years ago, a new process called oxygenic photosynthesis evolved. This is the same photosynthesis that you probably learned about in science class: cells convert CO₂ into plant material using energy from the sun, and they produce O₂ as a byproduct. The result was a massive increase in atmospheric oxygen, which was vital for the evolution of multicellular organisms.

Before the rapid expansion in oxygen, cells relied on anaerobic metabolism to generate energy and produce organic material. The general anaerobic "food chain" goes like this:

Complex molecules --> Sugars and amino acids --> Alcohols, acids, and acetate --> Methane (CH₄), carbon dioxide (CO₂), and hydrogen sulfide (H₂S)

Each step in that process is performed by diverse groups of organisms. The most familiar step is the transformation of sugars into acids, also known as fermentation. The acid produced depends on the microorganism, and the transformation also yields energy for the microbe.

The best known fermentation reactions are those that humans have harnessed for food production. Lactobacillus and Lactococcus produce the characteristic lactic acid in yogurt, and yeast ferment sugars into the alcohol we drink at bars and breweries. Kimchi production uses a variety of organisms, including both lactic acid bacteria and yeast as well as mold.

The exact composition of the community determines the taste profile of a fermented food. The specific alcohols and acids that are produced depend on both the organisms present, and the complex molecules that they eat. The unique combinations are responsible for the taste profiles of kimchi, yogurt, and other fermented products.

The dangers of oxygen

The rapid increase in atmospheric oxygen was a dangerous development for anaerobic microbes. When oxygen is used for aerobic cellular respiration, it is broken apart and transformed into H₂O and CO₂. But sometimes this process is incomplete, and individual oxygen atoms are left to roam around cells.

Single oxygen molecules are called free radicals, and they are highly reactive because of their unpaired electrons. Free radicals can attack proteins, DNA, and other cell components. Aerobic organisms have evolved specific enzymes that gather up these radicals and minimize the harm.

Anaerobic metabolism, on the other hand, does not produce oxygen free radicals. Many anaerobes did not evolve to produce these protective enzymes, because they weren't needed in the low-oxygen world. These organisms are thus highly susceptible to damage by free radicals, and many cannot survive prolonged encounters with oxygen. Some microbes protect themselves from oxygen exposure by living in anaerobic environments.

Anaerobic environments in nature

Anaerobic environments are all around us. They are even inside of us: portions of the human digestive tract are oxygen-free. Our bodies are home to a host of anaerobic microbes that help us break down food using that same basic anaerobic food chain.

In nature, sediments and biofilms are prime examples of anaerobic environments. In sediments, oxygen is rapidly consumed near the water-sediment interface, creating an anaerobic environment just a few centimeters below the surface. Biofilms are made of cells and complex proteins that build up in thick, dense layers. They form a barrier that it is very difficult for molecules, even small oxygen molecules, to diffuse through. The center of these biofilms can be home to anaerobic bacteria.

One key process in nature that is highly susceptible to oxygen is nitrogen fixation, in which microbes transform nitrogen gas from the atmosphere into forms that are usable by plants. The enzyme that performs the reaction, nitrogenase, is irreversibly damaged by exposure to oxygen at even very low levels. Microbes have found creative ways to avoid oxygen and maintain nitrogen fixing capabilities.

Some microorganisms live in completely isolated compartments called nodules, which form on the roots of plants. This represents a symbiotic partnership between microbes, which receive sugars from their host, and plants, which receive the newly-fixed nitrogen. Special enzymes called leghemeglobins (named for the legume plants where root nodules were first discovered) bind up oxygen and transport it out of the nodules, protecting the nitrogenases.

Microbes in the soil also fix nitrogen, by taking advantages of temporary pockets of oxygen-free space that form between soil particles. Water gets trapped in these spaces, called micropores, and the oxygen in the water is rapidly used up. This leaves the anaerobic nitrogen fixers with a space to do their work.

These microbes have also adapted to the temporary nature of these micropores by evolving mechanisms to control production of the nitrogenase enzyme. Oxygen levels in the environment signal to nitrogen-fixing organisms whether they should or shouldn't produce nitrogenase. This way, they don't waste resources making the enzyme when it will immediately be destroyed, but they are poised to start producing it as soon as the conditions become favorable.

Anaerobic processes in human-created systems: wastewater treatment and beyond

Humans have been using anaerobic processes to their advantage for centuries. As discussed above, food production is one of our most prevalent partnerships with anaerobes. Another is wastewater treatment, which utilizes anaerobic metabolism in several ways.

Secondary wastewater treatment involves anaerobic digestion of waste with large volumes of organic matter. The process generally follows the anaerobic food chain. Complex molecules like cellulose, proteins, and fats are broken down into simple compounds, which are further transformed by fermentation and additional processes. One of the major end products is methane, which the wastewater treatment plants often burn as a source of energy.

Tertiary treatment uses nitrogen cycling microbes in a two-step process. First, ammonia (NH₄), a byproduct of secondary treatment, is converted into nitrate (NO₃) in an aerobic chamber. The water then moves to an anaerobic chamber, where nitrate is transformed into nitrogen gas.

What other ways can humans harness the power of anaerobic microbes? Only time will tell! Anaerobic degradation of contaminants of concern like PFAS and pharmaceuticals has been observed in wastewater treatment facilities. It's only a matter of time until we discover even more anaerobic bacteria that are capable of amazing feats!

Want to learn more about how you can harness the power of anaerobic microbiology for your environmental projects? Reach out to AppliedMicrobio today!