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Life on Earth Part 1

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Professor Ricardo Cavicchioli, from the School of Biotechnology and Biomolecular Sciences at the University of NSW, delves into the third domain of life, the Archaea; an astonishing insight into life on Earth.     
Life on Earth can be divided into three main types, Bacteria, Eucarya (organisms such as animals, plants, yeast) and Archaea. All of the microbes do important things to keep the planet’s ecosystems healthy. Just like Bacteria, Archaea are single-celled and are very difficult to distinguish from bacteria, even under a microscope. Unlike Eucarya, Bacteria and Archaea do not contain a nucleus. Archaea were only recently discovered to belong to a separate domain of life, a result of the development of new techniques in the 1960s and 1970s that enabled people to distinguish Archaea from the other types of microorganisms. 

Billions of years ago there was an organism that predated those three lineages of microorganisms. Bacteria and Archaea evolved from this form and Eucarya probably from Archaea. Archaea have shared properties with the other domains, some (including metabolism) being similar to Bacteria and some (such as gene expression) being more like Eucarya. They also have some unique traits. Methane gas is produced exclusively by a group of Archaea known as methanogens.

Interestingly, unlike Bacteria and Eucarya there are no pathogens among the Archaea, so they can be considered as very friendly microbes. Microorganisms perform functions that are critical to life on Earth. The Earth’s resources including carbon and nitrogen are finite and have to be recycled like water. Indeed without the processes performed by microorganisms life on Earth would cease to exist even if only one of the critical groups of microorganisms was destroyed. The Archaea perform roles such as fixing carbon dioxide in the atmosphere and turning over sulphur and iron compounds, important parts of that recycling. The methanogens grow at amazingly diverse temperatures, some existing in Antarctica at sub 0°C and others at temperatures as high as 122°C. Those methanogens that live in places like hydrothermal vents actually eat inorganic matter including carbon dioxide, hydrogen and ammonia and produce organic matter – themselves. Since organic matter is the basis of life, the methanogens were crucial in times past in creating the sort of planet where larger life forms like plants and animals were able to grow.


The methanogen, Methanococcoides burtonii, was isolated from the bottom waters of Ace Lake where it is permanently dark, cold (1-2oC), anaerobic (no oxygen), methane saturated (due to methane production from methanogens) and reeks of hydrogen sulphide – an environment it is very happy to call home. Prof Cavicchioli developed M burtonii as a model for studying cold adapted Archaea and has  published widely about its mechanisms of adaptation. M burtonii is a cold adapted methanogen; others grow at temperatures as high as 122oC; and some colonise animals (yes humans!), and love ruminant animals. 

The numbers of microorganisms are staggering but because they are invisible we are unaware of them. One millilitre of water from a beach contains a million microorganisms - a miniscule fraction of the 10 (to the thirty) that all of the oceans contain. Fortunately for humans the microorganisms continue to perform their functions even when the environment is damaged. There are more microbial cells in a human body than human cells and it is the methanogens and bacteria in intestinal tracts that play vitally important roles. Ruminant animals like cows can only eat grass because the intestinal system enables the microbes to grow and live there. It is not the cows but the microbes that are able to break down the grass and produce nutrients for the cow. Similarly, in the human GIT, it is the activities of microorganisms that permit us to access much of the complex foodstuffs we ingest. Scientists are hoping to find ways to cultivate healthy microorganisms in our bodies, thus promoting better health instead of relying on antibiotics which kill many of our normal resident microorganisms. About 85% of life on Earth lives at temperatures of 5°C or less which means that a lot of the biosphere is very cold. This includes the deep oceans and alpine and polar regions, so there is a focus on Antarctic microorganisms in Professor Cavicchioli’s research.

In 2006 Prof Cavicchioli commenced expeditions to Antarctica to obtain samples to allow his group to determine whether their laboratory work provided real insight into what M. burtonii actually did in the environment.     
Ace Lake is a stratified, 25 m deep lake, with distinct zones: the top layers mix during the year and are exposed to light; a middle zone contains a thick (more than 1 m) layer of green sulfur bacteria that play a critical role in ecoystem function; the bottom layer is stagnant and smelly. By sampling microbes from throughout the depth of the lake, they were able to learn not just about M. burtonii, but discover what other microbes are present, who they choose to interact with, what functions they perform as a community, and start to learn how they will be affected by ecosytem changes – particularly global warming and introduced species.

Because these organisms have naturally adapted to the cold, humans can try to exploit some of the products that they produce. When we wash clothes or dishes, for example, we use harsh chemicals like bleaches and sodium hydroxide. Those chemicals could be substituted by biodegradable enzymes (a product of the Antarctic microorganisms) which would break down the soils and the stains without harming the environment in any way.

All the hundreds of lakes in the Vestfold Hills (near the Australian base, Davis) are marine derived, having been isolated from the ocean only 3-5,000 years ago. Each lake represents a unique time capsule where we can learn how the communities have evolved and adapted to a closed lake environment. Deep Lake is the deepest accessible point on the Antarctic continent (~55m below sea level) and contains the coldest water known to support life. Like the Dead Sea, it is hypersaline so that even when Winter air temperatures fall to -40C and the water to -20C, the water does not freeze.     

The high salt comes from water evaporating and leaving a salt concentrated, briney solution. Deep Lake is home to an amazing community of haloarchaea – salt loving members of the Archaea. Professor Cavicchioli’s group found the haloarchaea are very ‘promiscuous’ and readily exchange DNA with one another. Their studies highlight  the unique nature of Antarctic microbes and how susceptible they are to human influences, and why Antarctic life (including the dominant microbes) should be protected to permit long term study of their exceptional adaptations that permit life to thrive in such extreme ecosystems..

Between October 2013 and April 2015, the expedition Research Assistants, Sarah Payne and Alyce Hancock spent 18 months in Antarctica taking samples from Ace, Deep and Organic lakes (plus about 100 others) so that the research group could study the changes in the lake microbial communities throughout a complete annual cycle. Sampling throughout winter is a major logistical challenge.    

Polar regions have a very different light cycle to the rest of the world: largely one big night/day cycle with darkness prevailing in winter and 24 hour sunlight in summer. The samples collected brought the opportunity to learn how communities adjust to such marked changes in both light and temperature (from cold to very cold). The samples were obtained through considerable expedition funding from the Australian Antarctic Science Program. They now form the basis for major projects funded by the Australian Research Council through the Discovery Project scheme and the US Department of Energy through a Community Science Program at the Joint Genome Institute.

Microorganisms are separate single cells but there are instances where they clump together. In waterways that have slowed down, for example slime can form. That slime is clumps of microorganisms which have formed into macro organisms that are visible. These biofilms can form on the bottom of ships and other surfaces even inside bodies, like the biofilms in our mouths that are removed by brushing our teeth. 

Microbes respond to the changes that humans make and some of those consequences are unknown but others are known.
At places like Greta and Neath in the Hunter Valley acid mine drainage has occurred (see left), a direct result of the microbes growing in the dug up soil and releasing acid. Those microbes encourage others that are more acid tolerant to grow causing the waterways to become very acidic.
That acidity solubilises other harmful compounds, compounds we do not want in our waterways so locals try to neutralise the consequences with lime. 

Plants take about half of the carbon dioxide from the air, microorganisms taking the other half. It takes a really long time to create a fossil fuel like coal but it takes just moments for all that carbon to be released back into the atmosphere when those fuels are burnt. This is not a normal cycle and is completely unbalanced in the direction of release, which is why fossil fuels are creating so many problems. Microorganisms then have a critical role to play in keeping our planet healthy and, despite their size, are an important matter of life.

Professor Ricardo Cavicchioli was interviewed by Ruby Vincent for A Question of Balance and provided all images included. Summary text by Victor Barry, March 2016.

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Life on Earth Part 2

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