# 2.1 Uncovering life in extreme environments on Earth and beyond

Metagenomics bypasses one of the most severe limitations of classical microbiology: most microorganisms cannot be cultivated in the laboratory.

This limitation is particularly relevant for microbes living in extreme environments. An extreme environment is a habitat whose physical or chemical conditions (such as temperature, salinity, pH, pressure, radiation, or nutrient availability) cannot be tolerated by most known organisms but still support specially adapted forms of life. Organisms capable of living in these extreme environments are called extremophiles.

## Box 1 Extreme environments on Earth

Our planet hosts a variety of habitats with extreme physico-chemical conditions. You may not expect to find life there, but in reality, these environments are still home for many microbes.

Deep-sea hydrothermal vents are found along mid-ocean ridges at depths often exceeding 2,000 meters, where complete darkness, immense pressure, and steep chemical gradients prevail. Vent fluids can reach temperatures above 350°C and are enriched in reduced chemicals such as hydrogen sulfide, methane, and metals. Here, only organisms that use chemical energy rather than sunlight to produce organic matter can thrive and they form the base of complex ecosystems that include (besides microbes) also tube worms, crustaceans, and molluscs.

Hyper-saline environments, such as salt lakes, salt flats, and salterns (such as the Dead Sea), are characterised by salt concentrations far exceeding that of seawater. Such high salinity imposes severe osmotic stress to cells, disrupting cellular processes for most organisms. However, halophilic (salt-loving) microorganisms have evolved specialised adaptations such as highly charged proteins and compatible solutes keeping their cells stable.

Polar regions, including Antarctic ice sheets and subglacial lakes, are cold environments with permanently low temperatures, limited nutrients, and long periods of darkness. Microbial life persists within ice, snow, and liquid water trapped beneath glaciers by adopting slow metabolic rates, cold-adapted enzymes, and protective cellular structures.

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Figure 6 (interactive) Examples of extreme environments found on Earth.

By enabling the direct analysis of genetic material recovered from environmental samples, metagenomics gives scientists precious information about how life persists in these very particular places.

Researchers from China (Xamxidin et al, 2025) looked at the microorganisms living in Lake Barkol, a highly salty lake, by extracting the DNA from water and sediment samples.

The research identified more than 300 different bacteria and archaea. Archaea are a group of single‑celled organisms similar to bacteria, and they often live in extreme environments with very salty, hot, acidic, or oxygen‑poor conditions. Around 97% of the genomes could not be identified at the species level, indicating that the lake hosts a large amount of previously uncharacterised microbial life.

Metabolic reconstruction revealed the presence of diverse carbon fixation pathways occurring inside living cells, including the Calvin-Benson-Bassham (CBB) cycle and the Arnon-Buchanan reductive tricarboxylic acid (rTCA) cycle, and evidence for both nitrogen fixation and denitrification processes. Using metagenomic data, scientists also found that microbes sampled in water and sediment showed distinct ways of dealing with the high salinity of the environment: some allow salts to enter their cells, while other keep the salt out.

Studying life in extreme environments on Earth is also central to astrobiology. Places such as hypersaline lakes, deep‑sea hydrothermal vents, acidic hot springs, polar ice, and radiation‑exposed deserts resemble conditions thought to exist on Mars or planets beyond our solar system. Discovering that life can thrive under extreme cold, heat, salinity, pressure, or lack of sunlight shows that life’s limits are much broader than once assumed, expanding the range of environments considered potentially habitable beyond Earth.

Extremophiles reveal the mechanisms that allow life to persist under harsh conditions. By studying their metabolism, stress‑response systems, and energy sources, scientists learn how organisms cope with challenges such as dehydration, DNA damage, or energy scarcity. This helps astrobiologists predict what forms alien life might take – for example, microbes that rely on chemical energy rather than sunlight.

Extreme‑environment research also helps identify biosignatures: specific gas combinations, mineral changes, or metabolic pathways (such as carbon or nitrogen cycling) that are difficult to explain without the presence of life forms.

- Why is metagenomics particularly useful for studying microorganisms in extreme environments like Lake Barkol?

- Microorganisms living in extreme environments cannot be easily grown in the laboratory, and most of them cannot be grown at all. Metagenomics allow scientists to study their diversity and properties without needing them alive, and it is a fundamental tool to discover new organisms.

- The study found genes linked to carbon and nitrogen cycling. Why do these findings suggest that Lake Barkol is an active ecosystem rather than a biologically ‘dead’ environment?

- These cycling processes require living cells, enzymes, and energy, and they occur continuously in response to environmental conditions. In contrast, an environment devoid of life would show little to no evidence of such coordinated, enzyme-driven chemical transformations.

- How can extremophiles help scientists in their search for life beyond Earth?

- Extremophiles are important because they show that life can survive and remain active under conditions once thought to be uninhabitable. By studying how extremophiles obtain energy, protect their cells, and carry out metabolism in harsh environments on Earth, scientists can identify the possible conditions under which life might exist on other planets or moons. Extremophiles also help researchers recognise chemical or biological signs of life that space missions can look for beyond Earth.

Finally, metagenomics can help scientists discovering new genes and biological properties with applications in medicine and biotechnology.

A perfect example is the polymerase chain reaction, which you encountered in one of the previous sections: the Taq polymerase, the enzyme copying DNA during PCR, was originally found in bacteria living in hot springs.

OpenLearn - The metagenomics revolution: an introduction
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