Microbes living on the edge

The extremophiles, or “lovers” (from the Greek –philos) of extremes, are microbes that form communities in seemingly inhospitable environments such as: acidic hot springs, alkali peat bogs, salt lakes, deep sea hydrothermal vents, volcanoes, caves and glaciers.

As we found earlier in the course, environmental conditions such as temperature, pH, radiation and pressure can be problematic. Fancy bubbling away in a pool of thick mud so hot that water vaporises almost instantly, and so acidic that it would corrode metal? Or living under intense pressure at the bottom of the ocean in water so sulphurous and salty that, even though the temperature is below freezing, it’s still liquid? Certainly not, but the term ‘extreme’ is used solely from a human perspective. Extremophiles are incredible microbes that live on the boundaries of life. Many of the scientific (and rather unusual) names for these organisms relate to the environments from which they were first isolated or their particular super hero abilities. Each species has adapted to live in a hostile environment in unique ways. They have evolved enzymes, “extremozymes”, that have unusual properties, remaining active in temperatures that denature enzymes in microbes that have adapted to live in more moderate conditions.

The beautiful colours of Grand Prismatic Spring in Yellowstone National Park, USA, are the result of pigments called carotenoids produced by thermophilic bacteria and archaea. Very hot water (90°C / 189 F) constantly bubbles up from underground chambers in the centre of the spring and starts to cool as it moves to the edges. This creates a temperature gradient that suits different communities of microbes and results in concentric rings of colour. You can read about the Yellowstone rainbow hot spring on the Smithsonian Magazine Website.

Grand Prismatic Spring which shows the hot centre and concentric rings of colour

Figure 1: Grand Prismatic Spring in Yellowstone National Park © Jim Peaco, National Park Service [Public domain]

Thermus aquaticus, a thermophilic bacterium isolated from a boiling hot, sulphurous spring in Yellowstone National Park, USA, was the original source of the heat-stable Taq polymerase enzyme used in the polymerase chain reaction (PCR), a fundamental technique in modern molecular biology used to amplify a specific region of DNA (Figure 2).

Diagram of the polymerase chain reaction (PCR), which is used in molecular biology to amplify a specific fragment of DNA.
1) A reaction mixture that includes a double-stranded DNA template, single-stranded DNA primers, nucleotides and Taq DNA polymerase enzyme, is heated in a PCR thermal cycler machine to 94 to 98 degrees centigrade. The high temperature causes each double-stranded DNA molecule to separate into two single-stranded DNA molecules. This step is called denaturation.
2) The reaction mixture is cooled to less than 68 degrees centigrade. This allows the DNA primers to bind (or anneal) to the complimentary regions in the now single-stranded DNA templates. This step is called annealing.
3) The temperature is raised to 72 degrees centigrade, the optimum temperature for the Taq DNA polymerase enzyme to function. It creates a complimentary copy of the DNA template by moving along the template and adding nucleotides, and so each single-stranded DNA molecule is converted into a double-stranded molecule. This step is called elongation. A specific region within the DNA template has now been duplicated.
4) Steps 1 to 3 are repeated multiple times (typically 30 to 35 times). The reaction is exponential (i.e. one copy is used to makes two copies after cycle 1, which are used to make four copies after cycle 2, eight copies after cycle 3, sixteen copies after cycle 4, and so on). The final PCR reaction mixture will contain billions of copies of a specific fragment of DNA.

Figure 2: Diagram showing how the polymerase chain reaction (PCR) can be used to amplify a specific piece of DNA © Enzoklop CC BY-SA 3.0

Other extremophiles will only grow if the temperature is almost 100°C, like the hyperthermophilic archaea Pyrococcus furiosus which lives in hydrothermal vents at the bottom of the ocean (Figure 3: Left). Archaea have even been detected growing at <pH 0.3 in the world’s most acidic lake (Figure 3: Right).

Left: Black smoker at a mid-ocean ridge hydrothermal vent, Right: The crater lake of the Kawah-Ijen volcano

Click to expand

Figure 3: Left: Black smoker at a mid-ocean ridge hydrothermal vent © P. Rona. OAR/National Undersea Research Program (NURP); NOAA. Right: The crater lake of the Kawah-Ijen Volcano, Indonesia is <pH 0.5 due to a high concentration of sulphuric acid © CEphoto, Uwe Aranas CC BY-SA 3.0.

Deinococcus radiodurans (Figure 4) is a polyextremophilic bacterium, meaning it can tolerate multiple extreme environmental conditions; in this case radiation, cold and drought. It’s incredibly resistant to gamma radiation and can survive a dose of 15,000 Grays. For comparison a lethal radiation dose to a human is in the rather modest range of 2-10 Grays. Radiation causes damage to DNA and this bacterium has amazing abilities to repair it. Scientists are investigating its DNA repair enzymes to find out if they could be useful in medical treatments.

Transmission electron microgragh of *Deinococcus radiodurans*

Figure 4: Transmission electron microgragh (TEM) image of Deinococcus radiodurans © acquired in the laboratory of Michael Daly, Uniformed Services University, Bethesda, MD, USA [Public domain]

You’re probably thinking that extremophiles can only be found in far flung places and have no business being around humans, but you couldn’t be further from the truth. If you’ve ever suffered from stomach ulcers or even indigestion, your stomach, in all likelihood, has been colonised by Helicobacter pylori (Figure 5). Having strengthened its cell membrane, this spiral-shaped bacterium is able to withstand highly acidic conditions down to a pH of 2 or less; enough to corrode metal! Your gut is probably home to the likes of Methanobrevibacter smithii and Methanosphaera stadtmanae. These archaea use the hydrogen produced by other gut microbes (via anaerobic fermentation of carbohydrates) and produce methane, helping you to break down your food and keep you healthy.

Process of spiral-shaped bacterium causing a stomach ulcer

Figure 5: How the spiral-shaped bacterium ‘Helicobacter pylori’ causes a stomach ulcer. © Y_tambe dual-license with GFDL CC BY-SA 3.0. 1. The bacteria penetrate the mucus layer that protects the cells lining the stomach and attach to the cell surface. 2. The bacteria metabolise urea to produce ammonia, which increases the pH and helps them to avoid being damaged by the acidic digestive juices. 3. The bacteria replicate and form an infection focus. 4. The mucosal layer is damaged, which exposes the underlying epithelial cells to the acidic digestive juices, leading to cell damage, inflammation and ulceration.

Extremophiles truly are some of the most amazing organisms on Earth. Although they are inside, all around and underneath us, there is still little known about them and so much left to discover.

Share this article:

This article is from the free online course:

Small and Mighty: Introduction to Microbiology

University of Reading