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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 
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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.
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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
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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.’
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