Craig Venter aims to
revolutionise our understanding
of the microbial world and
the genetic riches it harbours.
When he visited Plymouth
recently, Kelvin Boot spoke to
him about his plans for the next
stage of an ambitious genomic
world tour.
In the wake of Challenger
S
orcerer II, Craig Venter’s bio- the waters of our own planet. This was the the ship was sailing into uncharted – or at
prospecting yacht, has embarked catalyst; he saw the possibilities that this least under-sampled – seas. A pilot project
on the European leg of her world hidden treasure trove could harbour, and was needed to prove the concept, and in
tour, bound for the Baltic, Black and came up with the idea of using a yacht as a typical Venter style – and against all the
Mediterranean Seas. This is her second sampling platform to harvest these genetic advice at the time – he chose the relatively
expedition, sponsored by the Beyster Family riches. nutrient-poor waters of the Sargasso Sea off
Foundation Trust and Life Technologies. Sorcerer II, a 95-foot yacht, furnished Bermuda as his first search area.
Craig Venter is perhaps best known as with all the equipment needed for its
the only man to have read and published explorations and a complement of scientists Unimagined diversity
his own genome, confounding the scientific to undertake its mission, is the flagship of Scientific logic suggested that a great
establishment and proving the effectiveness the J. Craig Venter Institute. It provided the diversity of life shouldn’t be expected where
of the novel approach to assembling perfect environmentally-friendly floating there are few nutrients. But even Venter
and reading genes known as ‘shotgun laboratory – big enough to cross oceans, was surprised by the incredible variety of
sequencing’. As if this wasn’t enough of an manoeuvrable enough to go wherever it life found during a short stay in Bermudan
achievement, he then turned his mind and needed to collect samples. waters.
his techniques to investigating life in the Like the voyages of exploration of old, When the samples were analysed, more
oceans.
It was the discovery and sequencing Preparing the filtered samples for freezing before analysis.
of an extremophile, deep-sea-vent-
inhabiting organism in the Pacific that
spurred his ambitions. Methanocaldococcus
(Methanococcus) jannaschii makes everything
it needs from the carbon dioxide, nitrogen
and hydrogen it finds in the heated waters
surrounding ‘white smokers’.
To be able to thrive in such extreme
conditions, these kinds of organism often
exhibit special features. In Venter’s mind
that meant two challenges; firstly, to find
out what genome could let them live in
such a difficult environment; and secondly,
to look closer and see if there were any
applications that might be useful to
humans.
Venter realised that where there was one
there would be others – there was a parallel
world with unknown life forms beneath
18 Planet Earth • Autumn 2009
So far, analysis of the material collected of modern science the number of discoveries
on that first voyage has uncovered 19 we have made greatly exceeds what was
million new genes and thousands of new done before,’ Venter says.
organisms. Among them, Venter hopes, ‘The Challenger expedition took twice as
will be the holy grails of carbon capture, long and travelled double the distance of the
bio-fuels, pharmaceuticals and other bio- Sorcerer II expedition and discovered around
products. 5000 new species; we are finding the same
His agile mind continued to ask in almost every sample,’ he adds. ‘They sent
questions, and it wasn’t long before the a dredge down and examined the catch with
relatively enclosed seas of Europe caught their technology, we are using the tools of
his attention; exploited by humans for DNA sampling and super-computers to
than 1.2 million new genes and more than thousands of years, fed by numerous rivers analyse the data. They could only see the
1800 species of microbes were revealed, and surrounded by large populations, large organisms; we’re filling in the gaps
including 148 previously unknown bacteria. these waters ought to have an even more with the microbes.’
Amongst the haul of genes were 782 new interesting assemblage of microbes. But just accumulating information is
rhodopsin-like photoreceptors – light- Sorcerer II arrived in Plymouth, UK, only half the picture. ‘In some ways we are
sensitive compounds. Could the microbes earlier this summer and coincidentally comparable to those early explorations, but
be making their own nutrients from found a mooring within a stone’s throw the collection is one thing. It was the totally
chemicals in the sea water and sunlight? and 178 years of perhaps the world’s best unique insight that Darwin added that
To put that number in context, less
than 200 photoreceptors had previously
been discovered in all species, and the total If a stretch of sea that was seen as relatively barren
number of genes previously known had just
been doubled. In such a small area, this was could contain such vast treasures of new species,
a staggering discovery. If a stretch of sea that
was predicted to be relatively barren could
what untold wealth was to be found elsewhere?
contain such vast treasures of new species,
genes and surprises, what untold wealth was known scientific voyager – HMS Beagle, really changed the world,’ Venter argues.
to be found elsewhere? which set sail from the same port and ‘The challenge is on us and others to see if
Bolstered by this initial success, the changed biological thinking for ever. The the same thing can happen with this massive
Sorcerer II expedition set sail from Canada historical link was part of the reason Venter amount of data we’re collecting.’
in August 2003 on a voyage that was to chose Plymouth as the starting point for the Venter’s world, beyond the microscope,
circumnavigate the globe. The Global European leg of the Sorcerer II expedition. was invisible to the scientists on board
Ocean Sampling (GOS) project lasted for ‘Sorcerer II is following in the wake of Challenger and to Darwin on the Beagle –
two years, sailed 32,000 nautical miles and the Beagle and what most marine scientists and, indeed, to most researchers until just
visited 23 different countries and island regard as the first real oceanographic a few years ago. The expedition will stop
groups on four continents. expedition, that of the Challenger. In terms and sample water every 200 miles, with the
Planet Earth • Autumn 2009 19
PML scientists join the Sorcerer II team to take water samples for analysis.
PML/H2O.tv/Dan Burton
expectation that 85 per cent of the genes Jack Gilbert and the PML team have been using massive computational power and
analysed will be completely new to science. doing great work that dovetails with ours; specially-developed algorithms.
Already the first expedition has taken the it’s natural to collaborate. We can help It is this technique, sequencing a whole
total of known genes from one million to with analysis, and they provide a wealth of sample rather than trying to search for
20 million. experience of the local situation. Putting our individual new organisms, that makes the
snap-shot together with their time sequences process faster and far more comprehensive.
The microbiology of Plymouth Sound makes absolute sense.’ Gilbert at PML is excited at the prospect of
The original expedition plied the waters of ‘We’ve been developing techniques over working with Venter.
the great oceans – the Pacific, the Atlantic, the last few years, spurred on by the work of ‘We know the oceans are changing and
the Indian – and travelled from pole to pole. Craig and the Global Ocean Survey being by cataloguing in this way, we can measure
But the seas close to home are just as likely carried out through the Sorcerer II,’ agrees and understand those changes,’ he says.
to reveal a plethora of novel organisms. Gilbert, a microbial ecologist at PML. ‘So ‘Micro-organisms do everything for us,
‘This second voyage will take us to the we’ve taken on board those technologies without them there is no other life, so it is
Baltic, the Mediterranean and the Black Sea and tried to apply them in UK waters; it essential to appreciate how they work and
where we expect the diversity will be equally increases the amount of information we can are affected by changes,’ he adds.
great, and totally different from what we collect and tells us about the wider ecology ‘As a molecular biologist what is really
have seen before. But without leaving the rather than just about single species.’ exciting is that we now have the ability to
dock we could take a barrel of water from After just a few days it was obvious the characterise the bacteria and the viruses,’
Plymouth Sound and discover maybe collaboration was going to be a great success’ Gilbert explains. ‘We think of those as bad
20,000 to 40,000 new ‘species’,’ Venter and Sorcerer II, with Venter on board, long things, but they may hold the answers to
argues. overstayed its planned time slot. Over the many of the challenges we now face – food,
But it’s not simply the prospect of more next couple of weeks teams of Sorcerer II disease, fuel, but most important to me is
new species and the Beagle connection that and PML scientists joined forces to collect that they are the key to understanding how
have brought Venter to Plymouth; he was sea water and the microbes it contains at the entire ocean fits together.’ ❖
also keen to work with the city’s research long-time-series sampling sites.
community, including the scientists of The samples are filtered on board and
Plymouth Marine Laboratory (PML). immediately frozen before being sent back
‘During the first voyage and through to the J. Craig Venter Institute (JCVI) labs MORE INFORMATION
this second expedition collaborating with back in the US, where the samples will be
local marine scientists gives us the context analysed. The filtered samples are jetted Kelvin Boot is a communicator and media
of ongoing scientific investigations,’ he through minute tubes that break up the consultant, working with Plymouth Marine
Laboratory, email: kelota@pml.ac.uk
says. ‘Here in Plymouth, for example, genetic material; it’s then put back together
20 Planet Earth • Autumn 2009