Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Non-coding DNA wikipedia , lookup
Genome evolution wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Molecular evolution wikipedia , lookup
Genetic engineering wikipedia , lookup
Community fingerprinting wikipedia , lookup
Microbial metabolism wikipedia , lookup
Evolution of metal ions in biological systems wikipedia , lookup
SOME LIKE IT HOT Deep beneath the surface of the earth where the water is aeons old, the temperatures are high and oxygen is non-existent, no life forms can exist. Correct? Absolutely not! Chesney Bradshaw investigates the minuscule organism whose preference for these extreme conditions has earned it the intriguing name of ‘extremophile’. TEXT BY CHESNEY BRADSHAW PHOTOGRAPHS BY TIM JACKSON A t a few thousandths of a millimetre long, it’s so tiny that it can only be seen with the aid of a powerful microscope. And with a lineage stretching back to prehistoric times, it’s older than most life forms on earth. So old, say scientists, that it is close to the base of the tree of life. The rod-shaped bacterium Desulforudis audaxviator exists in complete isolation and total darkness kilometres beneath the earth’s crust, where there’s no oxygen and the temperature is a toasty 60 °C. Unlike most other creatures, whose energy is derived from the sun, this microorganism feasts on sulphate and hydrogen, which are geologically produced by the radioactive decay of uranium, and on carbon and nitrogen extracted from the surrounding rocks. In short, Desulforudis has been equipped with such amazing survival genes that it was given the species name audaxviator (bold traveller), taken from Jules Verne’s Journey to the Centre of the Earth. Scientists also call it an ‘extremophile’. While it’s known that it has other heat-loving relatives such as bacteria that occur in deep-sea vents and hot springs, D. audaxviator’s adaptation to its environment is considered to be unique. Researchers have taken more than 10 years to find, examine, describe and catalogue the organism’s genome sequences, or DNA . Now, microbiologists and biochemists from the US and South Africa are investigating the use of extremophile genes to reduce pollution, tackle diseases and work wonders in food products. T ABOVE Back in the lab, doctoral student Walter Müller collects DNA samples from the extremophile bacteria Desulforudis audaxviator. Its genes may help unlock products in the fight against cancers, bacteria and viruses. OPPOSITE What do you do for a living? Van Heerden, colleague Professor Derek Litthauer and student Rudi Banyini prefer to spend their time several kilometres underground looking for bacteria that inhabit these extreme environments. he quest to go deeper to discover the basic limits of life led Tullis Onstott, a geosciences professor at Princeton University in the US, to conduct his research in South Africa, where the gold mines are among the world’s deepest. The university’s w w w. a f r i c a g e o g r a p h i c . c o m 31 Desulforudis audaxviator exists in ... total darkness kilometres beneath the earth’s crust, where there’s no oxygen and the temperature is a toasty 60˚C ABOVE With help from one of her students, Van Heerden collects water samples several kilometres underground. 32 AFRICA GEOGRAPHIC • m ay 2 0 1 0 The Life in Extreme Environments ( LEx EN) programme is supported by organisations such as the National Science Foundation and the National Astrobiology Institute, a NASA-funded research centre that designs instruments to detect subsurface rocks and groundwater on Earth in preparation for exploration of Mars. International collaborators include geosciences companies, specialised laboratories, universities and gold-mining companies in South Africa. Delving to some three kilometres below the surface, Onstott and his team took pristine fissure samples of water believed to be up to 40 million years old. Professor Esta van Heerden, a biochemist at the South African University of the Free State’s Depart-ment of Biotechnology, collaborates with the team. Since the 1920s, geologists working at oilfields in the US have maintained that chemical contaminants found in crude oil suggest bacterial life underground. Despite this, research into subsurface microbiology lay dormant until 1966, when researcher Thomas Brock discovered another heat-loving microorganism, Thermus aquaticus, in a hot spring in the Yellowstone National Park. A decade later, T. aquaticus was used to help develop the Polymerase Chain Reaction process, which rapidly replicates DNA. The biotechnology revolution that followed led to DNA sequencing becoming a multibilliondollar business. The search for subsurface extremophiles was revived. Researchers drilled boreholes in South Carolina, US, and developed methods to obtain samples from the depths. They confirmed the existence of subsurface bacteria living in high temperatures. Underwater, deep-diving submarines found cryptoendolithic (hidden within rock) organisms whose metabolism is driven by heat from a geothermal source. Onstott and his team followed strict safety procedures when handling the samples so that the microorganisms would not contaminate, or be affected by, life on the surface. (It has subsequently been confirmed that extremophiles are harmless to humans.) ‘People usually associate bacteria with spoiling food or disease in humans,’ said Van Heerden, ‘but these organisms are much lower down the food chain. In fact, many die when they come into contact with the earth’s atmosphere.’ In October 2006, Onstott and his colleagues published their findings in the journal Science. They had established the genome sequencing of the bacteria they’d harvested three kilometres below the surface in the Mponeng gold mine, where the water in underground fractures is estimated to be 15.8 million to 25 million years old. V an Heerden has lead the LExEN programme in South Africa since 2001, and during the following year her team and their US counterparts saw the first visual images of the cultured microorganisms. They have also acquired the techniques to extract DNA directly from the samples, circumventing the tradition of culturing the bacteria first. In 2007, Van Heerden’s team was awarded a R13.7-million research contract by BioPAD, a South African biotechnology initiative, and the Platform for Metagenomics was established. Focusing on the direct extraction of DNA from microbes in their natural environment, the platform also allows for laboratory manipulation to develop useful products or catalysts. This type of biological manipulation is known as environmental genomics: genes removed from prehistoric organisms are used to help create new products that may be used to fight cancers, bacteria and viruses. ‘The genes may even be candidates for HIV/Aids and anti-malaria drugs,’ Van Heerden says. ‘These organisms are stable at such high temperatures that we could also use them in regular industrial processes without spending lots of money on cooling, which is usually required,’ she continues. ‘For processes such as metal extraction, turnover could skyrocket.’ genes removed from prehistoric organisms are used to help create new products that may be used to f ight cancers, bacteria and viruses Historically, industrial and mining developments have produced large quantities of dangerous contaminants that pollute our groundwater. One of these, the heavy metal Cr (VI) or chromate, is a well-known carcinogen. Extremophile microorganisms are able to convert the chromate to the less toxic Cr (III) species far more efficiently than conventional chemical means. They can also consume iron, uranium and arsenic and convert harmful heavy metals and other toxic waste into more environment-friendly forms. ‘We can use them to clean up contaminated mining and industrial environments,’ Van Heer-eden elaborates. She suggests that the organisms could impact on future developments in much the same way that the enzyme discovered in T. aquaticus has helped to rapidly copy DNA. ‘That has been the biggest discovery in biochemistry and molecular biology during the past decade or two. It changed science,’ she says. Van Heerden admits that her imagination has been stirred by the effect that research into extremophiles is having on scientists’ grasp of the origins of life. ‘Through the research platform we will be able to understand deep-mine microbial populations and their potential application in the search for life in outer space. It is likely that, if life were to be found on other planets in our solar system, it may ABOVE Perilit vel ut laorpero exero exeros nit, sustion ex elenisim duisl do commy nibh ea faccum ea ad tie feugue feugait ulla aut iusto eraesto dolessisi. Tinfjnrybj ry jrku yt yu ktyuk y ukryuk ykuci tisl inciliquamet at, sim dolortie doluptat. LEFT Professor Esta van Heerden tests the oxygen content of water seeps in a deep underground goldmine. The bacteria she is looking for prefer anaerobic growing conditions, with no oxygen at all. resemble that which existed millions of years ago on Earth. ‘If we understand how the microorganisms work in the subsurface, we could help sustain our planet and possibly enhance life on other planets by helping to speed up evolution,’ she add. ‘It’s futuristic, but it fits with the theory of science and microbes in the subsurface.’ As scientists learn more about prehistoric microorganisms and the origins of life, this modern-day journey deep into the earth’s crust is proving more fruitful than Professor Lidenbrock could have ever imagined when he undertook his travels in Jules Verne’s Journey to the Centre of the Earth. As Van Heerden says, ‘Every day is like building a new puzzle. It’s intriguing.’ w w w. a f r i c a g e o g r a p h i c . c o m 33